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Bioconductor Changlog.
Tue, 13 Oct 2009
EBImage
fixed R CMD check memory leak (caused by a ReadImage() call after a drawtext() one); this was due to the MagickWandTerminus() destructor which also destroy MagickCore services (! see on ImageMagick wand/magick-wand.c for details)
metahdep
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
Rintact
updated the list2matrix function and man page
chipseq
Deprecate most of the context functions (moved to
GenomicFeatures). The context distribution stuff is ported, but untested.
bgx
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
yaqcaffy
yaqc.summary manual update
added summary(YAQCStatsObject) function
AnnotationDbi
adding to the TODO list
[/AnnotationDbi] permanent link
AnnotationDbi
Adds parameter for the inpIDMapper function.
This just adds another parameter so that you can choose to have the
final results limited to only one answer per initial ID even if you
map to something like a uniprot which may have many IDs for each
entrez gene ID. Default will still give you all of whatever you asked
for.
Added convenience function inpIDMapper
This function allows for easy mapping (using the appropriate
inparanoid packages) for IDs between species.
[/AnnotationDbi] permanent link
SemSim
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
some cleanup
changed interpretation of nsteps
LMGene
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
Another simulateReads rev.
Further speedup to simulateReads.
Further improvements to simulateReads function.
Improved performance of simulateReads.
Changed simulateReads function to use ShortReadQ class output
AnnotationDbi
This consolidates the INPARANOID_DB schemas into one.
By consolodating the INPARANOID schemas into one INPARANOID_DB schema,
I can now add more inparanoid packages without bloating up
AnnotationDbi any more than is strictly necessary...
[/AnnotationDbi] permanent link
chipseq
added alpha.hat to list of things computed
pdInfoBuilder
Prep'ing to add 2nd version of db-based annotation
[/pdInfoBuilder] permanent link
AnnotationDbi
end of testing.
testing
[/AnnotationDbi] permanent link
SPIA
small bug fix and vignette update
chipseq
Adjusted the number of bins in the density calculations.
AnnotationDbi
Fixes a small bug in SQLForge and expands inpIDMapper.
This fixes a small bug where SQLForge fails when organsisms don't have
unigene IDs, and also expands the number of species that inpIDMapper
should work for.
[/AnnotationDbi] permanent link
pdInfoBuilder
Fixed merging of POS and NDF files
[/pdInfoBuilder] permanent link
chipseq
one more mod
typo
one more set of tweaks
last piece
more updates to get the simulation code working
SPIA
updated pathway data by including interactions between genes and KEGG groups that contain at least one gene
AnnotationDbi
This adds support for worm, pig and chicken.
Adds code for planned support (October release) of these additional
organisms. These organisms are not supported at this moment.
[/AnnotationDbi] permanent link
RLMM
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
EBImage
New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1
AnnotationDbi
Adds convenience function for listing .db0 packages.
[/AnnotationDbi] permanent link
AnnotationDbi
Major overhaul for chip packages.
This checkin includes changes to allow chip packages to be lightweight
and instead depend on organism packages for their data. It also adds
organism support for rhesus monkeys, chimpanzees, Anopheles mosquito,
Arabidopsis and Xenopus laevis.
[/AnnotationDbi] permanent link
codetoolsBioC
Made error message more informative.
Stopped using ":::" operator since it doesn't support extraction from packages without namespaces.
Used Luke's suggestion to pass a modified collectUsageLeaf function into makeUsageCollector so the findGlobals search enters closures.
Recreate functions from scratch before passing to findGlobals function.
[/codetoolsBioC] permanent link
EBImage
Tried to provide a slightly more instructive warning when GTK+ cannot
be initialised at run-time.
GraphAT
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
maanova
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
CGHbase
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
SPIA
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Rintact
Fixed Rintact dependencies so package will pass check.
macat
fixes for enabling HTML output with .db data packages
macat
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
BicARE
This add BicARE, arrayMvout and affyContam to bioconductor.
cosmo
Fixed small bug in reverse complement calculation pointed out by Heejung
macat
fix to handle .db annotation packages
pdInfoBuilder
Cleaning up package, exporting only used classes
Added TilingFeatureSet2 class to handle 2-colors applications of tiling arrays. Redefined the FeatureSet class and sampleNames method. Removed unused class.
[/pdInfoBuilder] permanent link
RmiR
Addec package RmiR to svn
GraphAT
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
pdInfoBuilder
Improving support to Gene/Exon Arrays - gene level summaries
[/pdInfoBuilder] permanent link
BiostringsCinterfaceDemo
Additional examples and code clean-up
- read_solexa_fasta for reading two-line fasta files
- alphabet_by_cycle for tallying nucleotide counts by solexa cycle
- reorganize interface and documentation
[/BiostringsCinterfaceDemo] permanent link
AnnotationDbi
Just the documentation.
This check in adds some more documentation to the man pages to better
describe some of the new helper functions used in AnnotationDbi.
[/AnnotationDbi] permanent link
EBImage
minor typo in propagate man page
fixed minor typos in vignettes
fixed propagate man page and gradient computation
Removed confused text in the man page.
maanova
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
AnnotationDbi
normalized the default License field for packages made with makeAnnDbPkg()
[/AnnotationDbi] permanent link
chipseq
some antibody comparison code
added antibody comparison idea
maanova
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
yaqcaffy
Removed usage (or reference) to pstricks tex style in BioC vignettes.
chipseq
added an 'islands' argument for diffPeakSummary, plus misc changes
cosmo
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GraphAT
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
PLPE
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
codetoolsBioC
Edits based on Robert's comments.
Modified the finding of the origin of functions to better locate implicit S4 generic definitions.
[/codetoolsBioC] permanent link
pdInfoBuilder
Added warnings, so users don't expect SNP packages without CRLMM data to work with CRLMM
Added generic builders for SNP arrays. CRLMM wont work with these folks
[/pdInfoBuilder] permanent link
yaqcaffy
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
bugfixes and other updates
some new checkins
adding in some data sets to support simulation
minor tweaks to this script
minor commit - but lots has changed without version # changes
bgx
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
pdmclass
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
AnnotationDbi
Minor tweaks to enable chrlengths in Cross-db Bimaps.
[/AnnotationDbi] permanent link
[/AnnotationDbi] permanent link
widgetTools
removed quotes from do.call
chipseq
changes to length estimation and subset calculations
RLMM
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
codetoolsBioC
Added stats4 to the suggests field since it is used in man pages.
First pass at a codetools package extension.
[/codetoolsBioC] permanent link
AnnotationDbi
Adds ensembl for more species, fixes many man pages.
This update adds better support for ensembl IDs for many species, and
also updates several man pages to accurately reflect the more complex
origins of this data. In brief, when both NCBI and ensembl provide
data mapping entrez genes to ensembl gene IDs, we now will use data
from BOTH of these sources. However sometimes only one source is
available. In each case the manual pages have to be correct.
[/AnnotationDbi] permanent link
AnnotationDbi
This update adds new methods for filtering Bimap objects.
These new methods allow users more flexible ways of toggling the
filters for Bimaps that contain probes which may map to multiple
targets. Also more permissive filtering is now possible for
inparanoid based bimaps.
[/AnnotationDbi] permanent link
chipseq
Removing unused file.
PGSEA
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
pdmclass
Replaced usage of defunct method geneName with featureName in vignette.
Also quoted the component arguments to model.extract calls to conform with standard usage.
PGSEA
Updated convertSmc to work with Canine data
- moved Ruuid from "depends" to "suggests"
AnnotationDbi
Major overhaul of PFAM.db
These changes reflect a major overhaul of the new PFAM.db package to
squash bugs in there so that they won't burn users and also to provide
proper documentation.
[/AnnotationDbi] permanent link
panp
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
AnnotationDbi
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/AnnotationDbi] permanent link
PGSEA
Minor bug fix in aggregateExprs()
affycomp
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
EBImage
Added TODO on drawtext man page.
hopach
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affycomp
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
AnnotationDbi
Fixes a bad bug in SQLForge introduced by Refseq vers. #s
This adds some debug code, and also fixes a bad bug introduced when I
added code that attempts to automatically scrub version numbers from
[/AnnotationDbi] permanent link
widgetTools
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
pdInfoBuilder
Implemented changes to accommodate sequence methods that depend on biostrings/iranges. Improved templates so the final object passes check
[/pdInfoBuilder] permanent link
pathRender
Updated dependencies to drop unecessary warnings.
SemSim
t
Update probability table (10/02007)
hopach
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
sagenhaft
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
adding stuff for simulation
pdInfoBuilder
Added support to HT_HGU_133+ Array
[/pdInfoBuilder] permanent link
chipseq
minor updates
sagenhaft
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
BiostringsCinterfaceDemo
aligned with latest changes to the Biostrings C interface
[/BiostringsCinterfaceDemo] permanent link
panp
fix Rd issues found by Rdversion 2 parser
RLMM
Changed biocViews DNACopyNumber to CopyNumberVariants and SNPsAndGeneticVariability to SNP, GeneticVariability.
BicARE
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
pdInfoBuilder
Updated imports for Affymetrix Annotations v24, aka NA24
[/pdInfoBuilder] permanent link
EBImage
I fixed some formating and wordings in the installation vignette
chipseq
changes in methods etc
chipseq
minor update
more code for differential peaks
sigPathway
Updated dependencies to modern ".db" packages.
pathRender
Fixing man page links to graph package.
MassSpecWavelet
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/MassSpecWavelet] permanent link
maanova
checking in version 1.13.3
PGSEA
fixed Rd issues found by Rdversion 2 parser
RLMM
Removed usage (or reference) to pstricks tex style in BioC vignettes.
EBImage
2.7.8
- validImage in C, removed isImage in C
- merged IndexedImage class within Image, no IndexedImage class anymore !
- removed spurious '...'
- classUnion ImageX instead of Image !
- now Image supports non-numeric storage.mode (e.g. logical) !
- ImageCall instead of Call to check Image validity and storage.mode
- deprecated: matchObject, stopIfNotImage
chipseq
deleted stray code
cosmetic updates
chipseq
Add examples. Fix DLL loading. Should be ready for preview.
AffyCompatible
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/AffyCompatible] permanent link
affypdnn
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
chipseq
Bump version.
BicARE
Updated eSet objects and bumped package version numbers.
dualKS
fixed Rd 2 parser warnings
AnnotationDbi
Changes and bug fixes for making chip based pkgs.
These changes and bug fixes allow things to work properly for making
chip based databases and bundling these into packages. There is still
a minor issue with arabidopsis to fix. And then the intermediate
databases need to be bundled into packages for easy distribution and
the default paths set for these helper functions.
Wrapper functions for chip packages
This update adds wrapper functions for chip packages along with man
pages. This code still needs to be much more thoroughly tested and
there are still problems here with support for Yeast and Arabidopsis
which both still need to have the portion of their code that maps data
set up for the mapping of non-affy packages. But at least now it
should be possible to call a function, and have it make a database,
and then wrap that up into a chip based package. Organism based
packages are more monolithic and so are not really expected to need a
wrapper package. Although the code to make the sqlite files and the
packages for these is already here.
[/AnnotationDbi] permanent link
metahdep
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
chipseq
code for peak overlaps
chipseq
template hmm code
AnnotationDbi
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Fixed mget(c("GO:0018075","GO:0018075"),GOTERM) bug (the problem was in the .toListOfLists() function which was affecting the "as.list" method for GOTermsAnnDbBimap objects). Version bump.
[/AnnotationDbi] permanent link
yaqcaffy
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
LMGene
Removed usage (or reference) to pstricks tex style in BioC vignettes.
affypdnn
changes to accommodate adding a name space to affy
pdInfoBuilder
Ensuring correct class for transcript_cluster_id field Gene ST arrays
Ensuring correct class for crosshyb_type field Gene ST arrays
changing readPgf/readClf to readPgfEnv/readClfEnv
Fixing class nomenclature
[/pdInfoBuilder] permanent link
EBarrays
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
BiocCaseStudies
Changed biocViews entry of Statistics to Bioinformatics.
[/BiocCaseStudies] permanent link
affycomp
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
chipseq
more updates
updates
updates
code for 'poisson' regression
panp
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
EBImage
fixed noGTK support
minor
fix noGTK support in display.c
AffyCompatible
add aliases for [,.TypedAssociation,...
[/AffyCompatible] permanent link
chipseq
update
AnnotationDbi
Fixes bug in inparanoid mappings.
This was a bad bug that prevented these mappings from filtering out all
the non-seed regions properly.
[/AnnotationDbi] permanent link
pdInfoBuilder
Fixed bug that caused MM sequences to be inconsistent - particular case: offset 0 SNP [A/T] or [C/G]
Fixed bug which caused MM sequences to be inconsistent - nb: genotype calls via CRLMM are not affected
[/pdInfoBuilder] permanent link
chipseq
Removing unused file.
Slight change to a CTCF script.
chipseq
fixed vignette dependencies
added a draft vignette
updated DESCRIPTION
deleted data objects moved to GenomicFeatures, added demo chipseq dataset cstest
hopach
Replaced support of soon to be defunct class exprSet with ExpressionSet.
chipseq
added new document
PGSEA
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
hopach
new version of hopach package with C code for distance calculations and several other speed and memory improvements.
affypdnn
removed quotes from do.call
GeneR
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
EBImage
documentation Ops minor
minor
EBImage
"display", "animate", "writeImage" are now no longer generic functions,
but rather just simple functions. This is also fixes a bug that lead to
title=deparse(substitute(x)) in "display" always evaluate to "x" no
matter what expression the function was called with.
Added a request to fix the writeImage man page.
chipseq
changes to length estimation and subset calculations
chipseq
a directory for figures
DAVIDQuery
Bumped version to 1.3.1, fixed "gene2gene" discussion in the overview/vignette, and fixed the title and author info.
AnnotationDbi
This updates the manual pages for Annotation Packages.
The man pages for the Annotation packages had to be updated because of
improvements to R's check parser.
[/AnnotationDbi] permanent link
chipseq
Updated the read for CTCF and GFP alignments. Also updated the simulation code.
Updated the CTCF and GFP scripts to use alignments based on cleaned reads.
AnnotationDbi
Fixes a bug in inpIDMapper when the src IDs are Entrez Gene IDs
This just skips an unecessary mapping step when the src IDs are
already Entrez Gene IDs.
[/AnnotationDbi] permanent link
PLPE
This adds 6 new packages to the repository and manifest.
The new packages are: MEDME, edgeR, PLPE, logitT, ArrayTools and
microRNA.
affycomp
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
AnnotationDbi
Fixed bug where wrong type of ID causes ins. of spaces
This fixed a bug where R was automatically casting numeric IDs to be
numbers which would cause spaces to be inserted downstream when these
data would be stuck into the database.
[/AnnotationDbi] permanent link
chipseq
some cleanup
added a few plots for real_mouse
chipseq
added a 'merge' argument to diffPeakSummary
EBarrays
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
chipseq
code for summarizing subsets
cleaned up combineLanes
AffyCompatible
Decrease dependency on RCurl version
[/AffyCompatible] permanent link
AnnotationDbi
inpIDMapper() is now compatible with org.Sc.sgd.db
I thought that I had checked this in, but apparently I was mistaken.
This fixes the inpIDMapper function so that it depends on an available
(and upgraded) yeast package instead of on a package that we decided
against distributing.
[/AnnotationDbi] permanent link
EBarrays
Removed support for soon to be defunct class exprSet.
hopach
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
PGSEA
Version bump...
chipseq
added code for paired-end fragment sizes
Rrefdb
Standardizing reference to Artistic License 2.0.
EBImage
minor test hashing features added
dualKS
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
pdInfoBuilder
Fixed sorting schema for sequences
[/pdInfoBuilder] permanent link
preprocessCore
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/preprocessCore] permanent link
AnnotationDbi
Forgot to svn add the help file. How embarrasing...
[/AnnotationDbi] permanent link
chipseq
updates
sigPathway
Bug fix to support newer SQLite-based package annotations (e.g., hgu133a.db)
chipseq
moved sparse density calculation code into chipseq
use new coverage() interface
AnnotationDbi
Minor bug fixes for release of candidate 1.1.8
These include some small typo fixes to the .Rd files, corrections to
the author lists on some new packages and the usual required update to
the version numbers across the board.
[/AnnotationDbi] permanent link
chipseq
Add a first cut at the authors.
Use gdapply in estimate.mean.fraglen example. Clean up metadata in vignette.
Add examples. Fix DLL loading. Should be ready for preview.
yaqcaffy
modified patternmatching in getQCRatios and .namegrep3|5 functions
PGSEA
Fixed aggregateExprs() to work with ".db" annotation packages...
BiostringsCinterfaceDemo
Made changes required because of recent move of the Auto-Extending buffers (C level facilities) from the Biostrings to the IRanges package. Bumped version to 0.1.5
[/BiostringsCinterfaceDemo] permanent link
AnnotationDbi
Added Marc to the Author field. Updated dependencies. Version bump.
Clean up of the code in showQCdata()
Bug fix for shoqQCdata()
This time the bug fixes are actually in.
Fixed bugs in showQCdata()
This change just fixes the showQCdata function so that the counts are
displayed correctly.
Fixes a bug in the new shoqQCData function.
This function needs further work to get the mapped keys to be counted
correctly.
Cosmetic change only.
This adds a news section to the AnnotationDbi
This adds a news section to AnnotationDbi which will be used to
announce MAJOR "bullet point" changes that have been made to the
package since the last revision.
Modifications to schemas.
These are changes to the schema documentation so that they more
precisely align with what was in the sqlite files that are feeding
into AnnotationDbi. Also, code was added to
AnnotationDbi-internals.Rd so that it will not complain about the man
pages being in a sub-template within AnnotationDbi for the new
packages.
Applied Marc's big patch: switch to version 1.0 of the schemas + support for the Inparanoid packages + support for new PFAM.db + pkgname() function for displaying QC information. No version bump for now. inst/NEWS file is in preparation and will be added later.
[/AnnotationDbi] permanent link
AnnotationDbi
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/AnnotationDbi] permanent link
AnnotationDbi
Fixed slowdown bugs
These bugs only impacts the speed at which SQLForge does it's job.
The results will be the same. But if you are building ~ 700 packages,
you might appreciate this change.
Bug fix for increased AnnBuilder file format compatibility
This fix makes things more compatible for people who are using classic
AnnBuilder style files.
[/AnnotationDbi] permanent link
chipseq
added a dataset
EBImage
I have:
- made some wording fixes in the vignettes
- added a TODO file with suggestions
- tried to make the "hist" method more useful
hopach
fixed typo: extra line break in DESCRIPTION
SPIA
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
chipseq
trying to take some advantage of the class structure
adding some methods to compute coverage on collections of reads
added some more useful class structures
trying to fix up the coverage function
DE islands; plot coverage
a better show method for AlignedList
updating coverageSummary - some problem with getting max
to work with default settings
found a minor bug
EBImage
2.7.6:
- fixed dy instead of dx in lib_filterThresh L37 in nFramePix = (2 * dx + 1) * (2 * dx + 1); (bug submitted by Glenn Davis)
- tile, untile, thresh: works fine on md, Color
- vignettes build OK
- translate: check param input OK
- keeping correct storage.mode after binary operations on TrueColor images
- deprecated functions moved to deprecated.R
- vignette changes: (indexing a[,,,1] instead of a[,,1] and promote usage of rgbImage)
- unit test inst/scripts/test.R added
EBImage
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
sagenhaft
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
AnnotationDbi
Overloads the Term and related methods for GOTERM
This update overloads the Term, Ontology etc. methods for GOTERM so
that they can take IDs or GOTermsAnnDbBimap.
[/AnnotationDbi] permanent link
PGSEA
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
chipseq
added new document
Rintact
i have added the man page
i have added a new method to the package
EBImage
new EBImage dll
panp
fixed Rdversion 2 parser warnings
bgx
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
EBImage
I fixed typos in the description file.
RmiR
Standardizing reference to Artistic License 2.0.
GraphAT
supported again on wellington
AnnotationDbi
Bug fixes for sqlForge involving primarily fly and arabidopsis.
These bug fixes only affect the sqlForge portion of the codebase and
primarily are concerned with getting the output perfect for the sqlite
files generarted for flies and arabidposis.
Updating the license reference to reflect R standards.
[/AnnotationDbi] permanent link
panp
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
RLMM
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
PGSEA
Make two changes:
1) Fixed a typo in PGSEA2.Rnw that was preventing build of package.
2) Replaced support of soon to be defunct class exprSet with ExpressionSet.
codetoolsBioC
Quote Rkeywords when writing out NAMESPACE information.
Adding information on when the NAMESPACE information was created.
[/codetoolsBioC] permanent link
AnnotationDbi
Addition of code to package up intermediate DBs.
This checkin adds the code that will be used to make biannual updates
of the intermediate databases. These databases will be shipped out to
developers as very large R packages, and will allow us to ensure that
everyone has the correct intermediate database installed in the
correct place. One package is planned per supported organism. The
sqlForge code has been modified to find these databases as a default
parameter so that everyone should be able to just use biocLite to get
the latest intermediate DBs (if they want to make annotation packages)
and then to just use the wrapper functions to crank out .db packages
for supported organisms.
[/AnnotationDbi] permanent link
maanova
checking in version 1.13.3
PGSEA
Updated eSet objects and bumped package version numbers.
Rintact
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
RLMM
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
pdInfoBuilder
chipName and ALLELE fix
[/pdInfoBuilder] permanent link
MassSpecWavelet
fixed a few small bugs
[/MassSpecWavelet] permanent link
chipseq
binomial test example
support for counting overlapping peaks
MassSpecWavelet
update related with adding a smoothing function
add a smoothing function
Deleted MassSpecWavelet
Created directory MassSpecWavelet
Add the "peakThr" parameter to peakDetectionCWT function to accelerate the calculation speed.
Add the "peakThr" parameter to peakDetectionCWT function to accelerate the calculation speed.
Added a smooth function to estimate the peak amplitude, which will be used as peak filtering criterium.
[/MassSpecWavelet] permanent link
SPIA
Changed version no to 0.99.0
AnnotationDbi
Modified schema definitions to match 1.0
These schema definitions should now match what is planned for 1.0
including my new tables for ensembl and flybase_cg.
This adds files that were previously missing from the 1.0 schemas.
These still need more changes to be full 1.0 compliant. But at least
now they are here.
Update the schemas for human and rodents for new tables.
Added ensembl tables to these schemas so I have to also add this into
the schema definition.
Added maps for Flybase CG IDs and ensembl.
These changes add maps and fine tune the man pages for the ensemble
and the flybase CG IDs. Now users should be able to easily get the
IDs used by ensembl for mammals and fly packages.
Adds the man pages for the ensembl maps.
This just adds man pages for the planned ensembl maps with changes and
concessions as appropriate to context of whether its a chip package or
an organism based one.
Adds man pages for the new FLYBASE CG maps.
This adds a man page to the FLYCHIP.DB and the FLY.DB packages with
appropriate concessions.
[/AnnotationDbi] permanent link
AffyCompatible
Work around XML changes
- xmlValue.XMLAttributeValue
- xmlDoc(xmlNode)
[/AffyCompatible] permanent link
EBImage
EBImage.Rnw forgotten in previous commit
2.99.8
- new INSTALL
- new vignette
AnnotationDbi
Minor bug fixes for cross platform compatibility of sqlForge
These minor fixes should ensure that sqlForge will work better across
OS platforms when looking for the standard DB packages.
Fixed mget(c("969","969"),org.Hs.egGO) bug (was in "as.list" method for GoAnnDbBimap objects). Version bump.
[/AnnotationDbi] permanent link
BiocCaseStudies
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/BiocCaseStudies] permanent link
chipseq
documentation update
codetoolsBioC
Fixed situation when imported packages import symbols from other packages and export those symbols out again.
[/codetoolsBioC] permanent link
chipseq
updating the script
AnnotationDbi
This just adds the two new package listings to the internal file.
This ci is basically, bioconductor bookkeeping.
[/AnnotationDbi] permanent link
twilight
Changed biocViews entry of Statistics to Bioinformatics.
GeneR
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
EBImage
I made the example of propagate simpler.
minor DESCRIPTION changes
Rintact
Added an alias for translateNodeID method for intactGraph objects to man page to get package to pass check.
nnNorm
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
affycomp
Removed usage (or reference) to pstricks tex style in BioC vignettes.
EBImage
Remove unused BioConductor build options file.
pdInfoBuilder
Added vignette explaining how to build packages for several array types
Added diagn. messages. Fixed chipName method for NGS arrays
[/pdInfoBuilder] permanent link
EBarrays
fixed warnings about missing methods package declaration
EBImage
Added cursor position tracking in GTK image display
chipseq
Remapped to isochores.mm9, this time with all chromosomes.
included missing pieces in data
nnNorm
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.
RmiR
Change to use RmiR.Hs.miRNA
EBImage
export(show) back in NAMESPACE
fixed pseudo, apply.Gaussian deprecation error message in tests/test.R
Missed Rd files
2.7.15
- no warnings anymore in R CMD check
- S4 methods removed
- header and assert deprecated
- test framework added
- documentation updated
- morphKern, mkball and mkbox deprecated
- all '...' arguments removed
- horizontal slider and clean display.c code added
- zernikeMoments arguments 'pseudo' and 'apply.Gaussian' deprecated
- display and readImage argument 'colormode' deprecated
- display arguments: 'main', 'no.GTK' deprecated
- .ImageCall and ensureStorageMode functions removed
bgx
Fixed references
pdInfoBuilder
fixed template build error
clean up manuals and makePdinfoPackage, moved common code to functions in utils.R, added new package template (work in progress)
[/pdInfoBuilder] permanent link
chipseq
bugfix
nnNorm
NAMESPACE
add namespace and fix a no visible binding warning
EBImage
now compiles OK + TrueColor bug fix
fixes failed example because of removed slots
- storage.mode is forced to 'numeric' after binary operations
- new fast distmap method
- castAsNumeric and castAsInteger functions added
- display uses now NEAREST_INTERPOLATION for faster and more accurate zooms
- display refreshes now the pixel location when using the scrollbars
- display now zoomes twice or half, to avoid pixel non-dyadic pixel size
- new typedef numeric
- dilatation, erosion are now performed on 'numeric' images using 'numeric' structural elements
PGSEA
Minor fix to go2smc() and kegg2smc()
chipseq
working on new funs
added some more pieces
PGSEA
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
metahdep
added metahdep package to the repository
chipseq
added dataset with mm8 isochore definitions
EBImage
typo in propagate
now uses the original CellProfiler propagate() function
fixed propagate
chipseq
dump coverage
code for DE analysis of methyl data
chipseq
First pass at code speed up.
AffyCompatible
- make affxLicence less visible -- this licence is for the package, not
the user
- update [,.TypedAssocation,... methods for ... argument dispatch
[/AffyCompatible] permanent link
BiostringsCinterfaceDemo
trying to please 'R CMD check'
[/BiostringsCinterfaceDemo] permanent link
maanova
fixed Rdversion 2 parser warnings
CGHbase
Added scanDate slot to Biobase's eSet class, added functionality in affy to utilize the new scanDate slot and updated all the packages that create direct subclasses of eSet, ExpressionSet or NChannelSet.
pdInfoBuilder
Updated chrom info in featureSet for NGS and fixed pmChr accessor
[/pdInfoBuilder] permanent link
AnnotationDbi
Fixes minor bug with the package checking code.
This bug would have prevented some packages which legitimately might
have had some empty fields for GO terms (this came up with the Sakai
strain of E coli), from passing check.
[/AnnotationDbi] permanent link
AnnotationDbi
Major overhaul of PFAM.db
These changes reflect a major overhaul of the new PFAM.db package to
squash bugs in there so that they won't burn users and also to provide
proper documentation.
[/AnnotationDbi] permanent link
pdInfoBuilder
Much better support to Exon/Gene Arrays
[/pdInfoBuilder] permanent link
pdInfoBuilder
Updated vignette
Added warnings, so users don't expect SNP packages without CRLMM data to work with CRLMM
[/pdInfoBuilder] permanent link
chipseq
added file for DE peaks functions
AnnotationDbi
Fixes a bug in the display of chrlengths vectors
There was a bug in the creation of the chrlengths vectors that was
introduced with the 1.0 schema changes. Bug only affected the display
of the data and not the underlying data, so only AnnotationDbi needs
to be updated to clear this up.
[/AnnotationDbi] permanent link
yaqcaffy
added drosophila2cdf to data/morespikes.tab
AnnotationDbi
Bug fix for missing keys.
This fixes a problem introduced when the maps were enabled for
supporting probes that map to multiple targets. It basically fixes
Lkeys() and Llength() so that they return the correct (complete) key
sets on maps regardless of which mappings are "exposed" or "masked"
depending on their status as being probes that match multiple targets
or not. The Lkeys() and Llength() methods should always give the FULL
set of probes even when some of the values for those probes have been
masked by a filter.
This update adds new methods for filtering Bimap objects.
These new methods allow users more flexible ways of toggling the
filters for Bimaps that contain probes which may map to multiple
targets. Also more permissive filtering is now possible for
inparanoid based bimaps.
[/AnnotationDbi] permanent link
AnnotationDbi
Further changes to clean up the role of probeMappings.
ProbeXXX mappings are used by all the probe package schemas, and these
changes just clean that relationship up so that methods like
toggleKeys will be used only when appropriate. This change just makes
things safer for the end users.
Bug fix for missing keys.
This fixes a problem introduced when the maps were enabled for
supporting probes that map to multiple targets. It basically fixes
Lkeys() and Llength() so that they return the correct (complete) key
sets on maps regardless of which mappings are "exposed" or "masked"
depending on their status as being probes that match multiple targets
or not. The Lkeys() and Llength() methods should always give the FULL
set of probes even when some of the values for those probes have been
masked by a filter.
[/AnnotationDbi] permanent link
pathRender
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
macat
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
AnnotationDbi
minor tweak to man page
trying to do a little more cross-linking of the man pages
[/AnnotationDbi] permanent link
pdInfoBuilder
Implemented changes to accommodate sequence methods that depend on biostrings/iranges. Improved templates so the final object passes check
Fixed props of getGeometry-methods.R
Fixed template so packages created by pdInfoBuilder pass R CMD check
[/pdInfoBuilder] permanent link
AnnotationDbi
Updated to add CHRLENGTHS to arabidopsis packages.
[/AnnotationDbi] permanent link
yaqcaffy
sfs() overloaded to return a named numeric vector
MassSpecWavelet
removed white spaces from \item{stuff} {
[/MassSpecWavelet] permanent link
chipseq
code for human data
allow reading of older MAQ alignments
EBImage
2.7.22
- fixed a bug preventing from reading palette images in color
- deprecated all ImageMagick functions except blur, gblur, equalize, resize and rotate
- validImage now checks validity of arrays
- new doc for ocontour, translate, resize, rotate , flip, flop
- new examples for makeBrush
AnnotationDbi
Exported the AnnObj class so people can extend the AnnDbBimap class in their own packages without getting a warning. Bumped version to 1.5.19
[/AnnotationDbi] permanent link
bgx
Added header declarations to bgx_frontend.cc to make it compatible with gcc 4.3
AnnotationDbi
Adds support for Canine, Bovine and bug fixes for Arabidoposis.
Adds code to support making Canine and Bovine packages, also there are
some minor changes to how Arabidopsis packages will display the
multihit mappings to be more precise about what is actually in the
package.
[/AnnotationDbi] permanent link
pdmclass
Changed API of pdmClass() by adding keep.fitted = TRUE. This allows the plot() and predict() functions to work when using many samples (the default for fda() is to set keep.fitted to FALSE if there are too many samples).
EBImage
Added references to distmap man page. Added '???' to the description
of the obscure 'exact' argument.
I also fixed a typo that upset R CMD check in filter2.Rd
Added a comment to the man page.
Removed the methods with 'missing' signature, we do not want them.
I fixed wordings in man pages:
distmap.Rd
filter2.Rd
Added some more to our heavy list of TO DOs
and tried to make the mkball function a bit more useful.
yaqcaffy
Replaced reference to defunct class exprSet with ExpressionSet.
macat
Standardizing reference to Artistic License 2.0.
SPIA
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
MassSpecWavelet
Add an example (adding absolute peak amplitude filtering) of peakDetectionCWT function
[/MassSpecWavelet] permanent link
chipseq
added a simulation example as well
chipseq
Relaxed the min score requirement on the PWM matching.
sagenhaft
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
chipseq
extendReads per-strand bugfix
trying to sort out some discrepancies
added in a summarizeLane2 - seems that we were ignoring
chromosome lengths, and working with the largest observed match.
added a class for the list representation of AlignedReads
Rintact
I have added a new function to parse the xml files
AnnotationDbi
adding to the TODO list
started a TODO list here
[/AnnotationDbi] permanent link
AnnotationDbi
Fixed rare bug that can happen when an ID is a very long integer
Fixed a rare bug that can happen where a very long integer is the ID.
When this happens R can promote this to a double before passing it to
SQLite which will then add an unwanted .0 extension onto the end of
it. Now Sqlforge will check for such IDs and cast them (but only if
needed).
[/AnnotationDbi] permanent link
AnnotationDbi
Updates to SQLForge and a better error msg for mget.
Part of this update just changes the AnnotationDbi mget message to
look more like what is expected based on what its parents msg looked
like. The other part overhauls the part of the code that does the
initial mapping for SQLForge so that it will not write out
indermediate files. This step was uneccessary and generally just a bad
idea that was causing bugs on the windows platform. The new code
should be more robust to cross platform issues.
[/AnnotationDbi] permanent link
Rintact
Fixed up the package so that it builds and passes check with 1 warning. Will fix the warning in the next couple of days. Will also deprecate the package in the next couple of days since RpsiXML will replace it.
AnnotationDbi
Major overhaul for chip packages.
This checkin includes changes to allow chip packages to be lightweight
and instead depend on organism packages for their data. It also adds
organism support for rhesus monkeys, chimpanzees, Anopheles mosquito,
Arabidopsis and Xenopus laevis.
[/AnnotationDbi] permanent link
AnnotationDbi
fixed typo in the SQLForge vignette (collumn == column)
[/AnnotationDbi] permanent link
pdInfoBuilder
Removing un-needed classes
[/pdInfoBuilder] permanent link
chipseq
Fixed the man page for subsetSummary by adding documentation for previously undocumented argument.
Switched from using direct slot access to accessor functions for AlignedRead objects.
Fixed the (position, strand) conversion in estimate.mean.fraglen methods for RangedData and AlignedRead objects.
BiocCaseStudies
a couple of glitches, hopefully repaired
fixed little issue with line breaks function
[/BiocCaseStudies] permanent link
affypdnn
Moved 2 of the packages in Depends to Suggests
chipseq
minor updates
code to load compiled so
speedup of some computations using C
nnNorm
fixed examples for the compNorm, since the new boxplot requires vectors only
GeneR
Removed reference to non-existent header file from src/readLocation.cc.
chipseq
support for strand-specific extending of reads, renamed growSeqs to extendReads
PGSEA
Updated NAMESPACE, man page and DESCRIPTION files.
This update just fixes some problems created by the switch to the
newer kind of annotation packages.
pdInfoBuilder
Bug fixes so that this will hopefully pass check.
[/pdInfoBuilder] permanent link
sagenhaft
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
pdmclass
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
updates
added a man page
process CTCF data
updates for course; contextDistribution still has bug
yaqcaffy
changes in morespikes.tab - addition of ricecdf spike probes
EBImage
Added 'seed.centers' argument to 'propagate' that specifies whether dot-sized seeds located at the centers of the original seed objects should be used instead of finite sized seed objects.
panp
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
twilight
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
widgetTools
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
added some material
added name for height of peak
GraphAT
Fixed a data help file example so package passes check.
CGHbase
Adds CGHbase and CGHregions to Bioc 2.3 repository.
EBarrays
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
dualKS
Changed biocViews entry of Statistics to Bioinformatics.
hopach
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
chipseq
Added script for finding CTCF binding sites in mouse genome.
arrayMvout
third times the charm
oops
fixing up the links
AnnotationDbi
Fixed bad but subtle bug in SQLforge.
This fixes a bad bug in SQLforge that would under certain rare
circumstances, map the wrong type of indentifier into the entrez gene
field. Now the code does a better job of making sure that when it has
an alternate ID, to find a correct entrez gene id if one can be found
and stick that into the entrez gene field.
[/AnnotationDbi] permanent link
pdInfoBuilder
Fixing documentation and adding generic builder for Affymetrix SNP/CNV arrays
Added some dontrun tags around two man page examples since they show how to interact with non-existant files.
Also, cleaned up the initialize methods a little to hopefully avoid problems when instanciating objects.
[/pdInfoBuilder] permanent link
LMGene
Replace usage of defunct classes exprSet and phenoData with ExpressionSet and AnnotatedDataFrame.
AnnotationDbi
Improvements to the org.Sc.sgd.db package.
These changes add new mappings to the org.Sc.sgd.db package for Entrez
Gene IDs, Refseq accessions, SGD accessions, and Uniprot IDs.
[/AnnotationDbi] permanent link
CGHbase
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
AnnotationDbi
Adds convenience function for listing .db0 packages.
[/AnnotationDbi] permanent link
widgetTools
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
pdInfoBuilder
Fixed bug in UnitTests for SNP 5/6
Fixed bugs in UnitTests
[/pdInfoBuilder] permanent link
maanova
forgot to add one part of the documentation for the new matchDataToDesign parameter. fixed now
maanova
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
bgx
Removing unused .BBSoptions file.
EBImage
2.7.11: no ImageX object anymore
updated TODO list, based on WH comments
BiocCaseStudies
empty inst created warning
added BiocCaseStudies package
[/BiocCaseStudies] permanent link
pdInfoBuilder
Adding support to Affymetrix GeneST Arrays
[/pdInfoBuilder] permanent link
sagenhaft
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GeneR
make it compile on openSUSE 11.0/gcc 4.3.1
hopach
Bumped version number
AnnotationDbi
removed quotes from do.call
Major change to SQL.R. Now Bimaps can join across DBs.
This updates AnnotationDbi so that Bimaps can be generated across
SQLite databases from multiple different installed packages.
Providing that the databases are indexed appropriately, there does not
seem to be a huge time penalty to such shenanigans, but there is still
some performance lost when doing this (on the order of a tenth of a
second for most maps tested). However this will hopefully be offset
by the fact that we will no longer have to have data in all of the
chip packages which is identical to the data in all our org
packages...
[/AnnotationDbi] permanent link
AnnotationDbi
preemptive bug fixes for inpIDMapper.
These are some code changes that will be needed once I have updated
the org.Sc.sgd.db package database to have a few new flavors of
mappings. This should allow this code to work with the new database
once I have it ready.
[/AnnotationDbi] permanent link
pdInfoBuilder
Multiple fixes: tiling ngs with XYS, missing fields on tables
[/pdInfoBuilder] permanent link
chipseq
script to read data and save as rda files
bugfix
CGHbase
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
affypdnn
Modification to make R CMD check run faster
- Added dataset with precomputed values
- Added man page for that dataset
- Bumped version number
EBImage
is(x, 'Image') instead of if(class(x)=='Image')
updated man pages
chipseq
Added verbose argument to shiftApply and switched basesCovered function over to use it.
EBImage
Removed spurious library lWand in configure.ac since Magick-config does a good job. This fixes the fact that EBImage didn't compile with ImageMagick 6.4.x (because lWand has been renamed to lMagickWand). I've forgotten to increase the version number in DESCRIPTION.
Removed spurious library lWand in configure.ac since Magick-config does a good job. This fixes the fact that EBImage didn't compile with ImageMagick 6.4.x (because lWand has been renamed to lMagickWand)
LMGene
Changed biocViews entry of Statistics to Bioinformatics.
preprocessCore
(1.1.4) remove extranous code comment
[/preprocessCore] permanent link
chipseq
changed extendReads to be faster
AnnotationDbi
normalized the default License field for packages made with makeAnnDbPkg()
[/AnnotationDbi] permanent link
AnnotationDbi
Bug fix for unigene/SQLForge
Fixes a bug that would cause problems for people using only unigene
IDs and SQLForge.
[/AnnotationDbi] permanent link
sigPathway
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
chipseq
Minor typo fixes to man pages.
Removing empty R file.
BicARE
bug fix in print.biclustering
AnnotationDbi
More updates to the manual pages.
[/AnnotationDbi] permanent link
arrayMvout
Changed biocViews entry of Statistics to Bioinformatics.
EBImage
Fixed some wordings in the propagate man page.
AffyCompatible
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/AffyCompatible] permanent link
pdmclass
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
AnnotationDbi
Adds a vignette for SQLForge, and some bug fixes.
This checkin adds a vignette for the newer SQLForge functions as well
as some bug fixes for some of the populate functions so that they can
correctly build their databases in the specified directories. Also, a
much shorter example file was added to cut down on the time needed to
check the new vignette.
[/AnnotationDbi] permanent link
hopach
hdist class and methods
Rintact
I have changed my e-mail so that it matches with the bioc-devel list server
chipseq
Added an IntegerList method for estimate.mean.fraglen.
Fixed a typo bug.
Added a RangesList method for estimate.mean.fraglen. Bumped version number.
Rintact
Fixed man page warnings
SPIA
small fixes
AnnotationDbi
These changes add support for Plasmodium falciparum
These changes add support to make databases and organism level
packages for the malaria parasite Plasmodium falciparum.
[/AnnotationDbi] permanent link
AnnotationDbi
Directory checking and refseq bug.
Fixed bug that happened when refseq IDs were uses as the primary
ID. And also added checking to wrapper functions to let users know if
they are trying to write a database into a place that does not exist
yet. These changes only affect SQLForge.
[/AnnotationDbi] permanent link
EBImage
More TODO on Zernike
zernikeMoments function and man page: What is the 'apply.Gaussian =
TRUE' argument doing? It seems bizarre. Does it make sense?
Forgot this at commit before.
I tried to clean up I/O functions and man pages.
EBImage
2.99.5
- channel OK
- paintObjects, drawtext OK
- colors.c removed
- doc: watershed
- simpler combine
minor test
minor test
EBImage
spurious print() in mkball removed
Rintact
I have updated the Description file and Namespace to try and avoid dependency collisions
macat
Replaced usage of newly defunct phenoData class and geneName method with AnnotatedDataFrame and featureName respectively.
BiocCaseStudies
Revert to how it was before the previous commit - since that change was
silly, sorry.
as a character vector.
[/BiocCaseStudies] permanent link
AnnotationDbi
More improvements to the Bimap documentation.
[/AnnotationDbi] permanent link
yaqcaffy
added a 'which' argument to yaqc.plot for individual QC graphs - added summary in exportMethods - updated dependecy for simpleaffy (>= 2.19.3)
AnnotationDbi
More convenient access to author info. via SQLForge wrappers.
This patch makes it easier to add maintainer and author information to
generated packages using the SQLForge wrapper functions.
[/AnnotationDbi] permanent link
EBImage
outline method added
chipseq
drop message
more bugfixes
fix bug introduced in r38544 when moving uses of coverage() to new interface
AnnotationDbi
Adds support for a new org package for yeast.
The previous org package for yeast was org.Sc.sgd and was based on the
SGD, which is sensible because that is the standard for that
community. This package is based on NCBI data and is an org.Sc.eg
package, which should hopefully reduce some of the complaints I get
about there not being an eg based yeast package. Also, we needed a
package to map the standard yeast ORF IDs to both EG and uniprot IDs,
and neither of these is available at SGD.
[/AnnotationDbi] permanent link
affypdnn
typos in the vignette
BiocCaseStudies
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/BiocCaseStudies] permanent link
EBImage
Improvements and bug fixes to 'propagate' (bug did not affect its performance, but made the code a bit confusing)
EBImage
2.99.7
- stackObjects OK
2.99.6
- doc: propagate, combine, tile, untile, rmObjects, reenumerate, hullFeatures
hopach
Housekeeping: removing INDEX files that are generated during the build process.
EBImage
minor fix for Windows build and holes.png file added (needed for floodFill example)
pdInfoBuilder
Cleaning up pkg
Improved support for NimbleGen Expression Arrays
[/pdInfoBuilder] permanent link
EBImage
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/preprocessCore] permanent link
AffyCompatible
minor typos
[/AffyCompatible] permanent link
chipseq
updates, and some preliminary neg binomial calulations
twilight
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
AnnotationDbi
Some improvements to the Bimap documentation (more to come). Version bumped to 1.3.6
[/AnnotationDbi] permanent link
dualKS
This adds dualKS to the package repository.
BUS
Added package BUS to svn
chipseq
code for fibroblast comparison
pdInfoBuilder
Replaced XDataFrame with DataFrame to reflect changes in IRanges.
[/pdInfoBuilder] permanent link
EBImage
Some more edits, and FIXMEs, for vignette
chipseq
bugfix etc.
Added usage of the new seqlengths function.
pathRender
try to eliminate warnings in doc
AnnotationDbi
Don't want to forget the version bump.
Bumped to 1.1.11
Remove limitation of metaDataSrc.sqlite
There are a number of bug fixes in this patch, but the most important
change is that there is no longer a requirement that a sqlite database
have an entry in the local metaDataSrc.sqlite file. This change is
critical to allowing users to make custom packages.
[/AnnotationDbi] permanent link
BiocCaseStudies
a couple of glitches, hopefully repaired
[/BiocCaseStudies] permanent link
nnNorm
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
EBImage
New EBImage.dll compiled with R2.7.0, GTK 2.12.9 and ImageMagick 6.4.1
AnnotationDbi
Removed old dependencies for GO and hgu95av2
There were some examples in the vignette of how we used to do things.
These have been set to eval=false and the dependencies have been
[/AnnotationDbi] permanent link
cosmo
Updated email address of maintainer
GeneR
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
code for DE analysis of methyl data
code to read in MAQ alignments of 54-cycle run
some updates
BiocCaseStudies
updated dependencies
[/BiocCaseStudies] permanent link
chipseq
update for myotubes
bgx
Merged -r33827:r33829 from release branch
chipseq
peak modeling updates
chipseq
minor updates
EBImage
finalized frameDist with distance, dot product and Pearson correlation
AffyCompatible
further XML work-around
- unconditionally define xmlValue.XMLAttributeValue
- use .xmlDoc, which checks first that the node is not already an xmlDoc
[/AffyCompatible] permanent link
pdInfoBuilder
Attempt to add an extra SNP/CNV level class
[/pdInfoBuilder] permanent link
codetoolsBioC
Added append argument to writeNamespaceImports and fixed code so it can write to a file.
[/codetoolsBioC] permanent link
affypdnn
Propagated fixes to the changes made in the release 2.2 branch
(revision 31982)
MassSpecWavelet
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/MassSpecWavelet] permanent link
arrayMvout
doc for spikQA
12 x 9
introducing fig3map
various
small structures
nnNorm
Removed usage (or reference) to pstricks tex style in BioC vignettes.
AnnotationDbi
Removed the some unnecessary comments from NAMESPACE.
[/AnnotationDbi] permanent link
pdInfoBuilder
doc change indicating parms_store instead of data_store for certain components
[/pdInfoBuilder] permanent link
PLPE
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
chipseq
update
frag length est updates
minor cleanup
GeneR
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
twilight
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
yaqcaffy
change in merge.yaqc function - only one log, target and arraytype (identical) attributes are kept
BiocCaseStudies
no non-db annotation packages left
[/BiocCaseStudies] permanent link
chipseq
Fixed the (position, strand) conversion in estimate.mean.fraglen methods for RangedData and AlignedRead objects.
Added estimate.mean.fraglen method for AlignedRead objects.
Removed unused variables in C code.
Made estimate.mean.fraglen an S4 generic with methods for list, GenomeData, and RangedData.
Added some argument checking to basesCovered, densityCorr, and sparse.density.
Added NAMESPACE imports to protect against improper method selection.
Bumped version number.
sigPathway
Changed biocViews entry of Statistics to Bioinformatics.
pdmclass
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
PGSEA
Simple change to fix depreciation of library(GO)
chipseq
Minor code change.
affycomp
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
codetoolsBioC
Fixed comments in writeNamespaceImports.
Added Depends comment to writeNamespaceImports output as well as added argument width to be used by strwrap.
[/codetoolsBioC] permanent link
pdInfoBuilder
pass check -- ST seed needs more doc
[/pdInfoBuilder] permanent link
EBImage
Added the 'untile' function that splits a tiled image (as they often come from microscopes) into a stack of individual frames
BiocCaseStudies
cleaned up Description
[/BiocCaseStudies] permanent link
chipseq
exploratory plots
BicARE
Changed biocViews entry of Statistics to Bioinformatics.
preprocessCore
(1.3.2) R_subColSummarize are now exposed at the C level
[/preprocessCore] permanent link
yaqcaffy
fixed bug in .plotdata function
AnnotationDbi
Cleans up the parameter names and input for SQLForge.
The param "ll" has been changed to "eg" for SQLForge since they are
not called locus link IDs anymore (so why name parameters after a name
people are forgetting in new code?). Also there is an issue that can
crop up with refseq IDs if the user is not paying attention and leaves
on the version numbers to these IDs. For Refseq IDs, only the
accession part of the ID is actually matched to a gene, and some
vendors give IDs that do have the version number attached while others
trim them off. Therefore our DBs always deal with these IDs with the
extraneous stuff removed. However since none of the databases use
these IDs, it also becomes impossible for any database to match on
them if the version numbers have not already been not clipped off by
the user (when the IDs have been provided by a vendor who leaves them
on), so there is now some "auto-cleanup" that SQLForge will do if the
user feeds refseq IDs as a primary ID that are still not trimmed of
their version numbers.
[/AnnotationDbi] permanent link
chipseq
Removed unneeded geneplotter dependency.
pathRender
fixed name space import problems
affycomp
Removed pch from matplot in affycomp.figure6a
panp
Updated eSet object and bumped version number.
AffyCompatible
Fixed typo in DESCRIPTION file (Microarry -> Microarray).
[/AffyCompatible] permanent link
AnnotationDbi
Removed code for redundant indices.
This removes many redundant indices from the SQLForge code. This
should reduce the size of the databases somewhat while not impacting
performance.
[/AnnotationDbi] permanent link
AnnotationDbi
This update adds support for multiple probe mappings in chip packages.
This update will add multiple mappings for all probe based (chip)
packages. It will also provide a new method to unmask these mappings.
This is all documented in the updated AnnotationDbi vignette.
[/AnnotationDbi] permanent link
chipseq
Changed biocViews entry of Statistics to Bioinformatics.
copyIRanges(a, b) is equivalent to Views(b, a) and should be removed eventually. For now made the appropriate changes to make it easy to remove that function.
Added aliases for methods.
Fixed some man pages to match underlying code.
chipseq
and bump version number
starting to add some man pages
affycomp
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
pdmclass
Fixed small bug in pdmGene() function.
codetoolsBioC
Added comment to output that provides a list of package imports.
Added more documentation to the details section of the writeNamespaceImports function.
Adding subscripting methods to the list of non-standard names to quote.
Adding quote and ignoreAllBasePackages arguments to writeNamespaceImports.
Added append argument to writeNamespaceImports and fixed code so it can write to a file.
[/codetoolsBioC] permanent link
chipseq
updates to accommodate simulating
need to revert that change
updated the quality score data
minor update
cosmo
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
AnnotationDbi
Final changes for Worm, Pig & Chicken, adds new info. to most pkgs.
This update adds support for Worms, pigs and chicken. It also adds
suport for uniprot IDs to most packages, ZFIN IDs to zebrafish
packages, and Wormbase IDs to worm packages. Finally, it also adds a
CHRLOCEND mapping to most packages which will allow the inclusion of
gene ending locations into most annotation packages in addition to the
usual CHRLOC mapping that already provides the start positions.
[/AnnotationDbi] permanent link
EBImage
2.7.16
- fixed warnings due to unused variables in C code
- fixed a drawtext bug which prevented EBImage to be checked on R 2.9.0
- fixed floodFill example by restoring inst/images/holes.png
AnnotationDbi
Minor adjustments.
This change just removes RSQLite and DBI from the search path.
DBI and RSQLite have both been imported here for some time, this just
gets them out of the DEPENDS field, and cleans up any in-package
consequences.
[/AnnotationDbi] permanent link
EBImage
Major update:
- functions copy, .isCorrectType, .correctType have been removed
- multidimensional arrays are now handled
- new color mode Color added
- functions getNumberOfFrames, translate added
- signature combine has been changed
- validity method added
- file filters.R renamed in magick.R
- file spatial.R added
- abind dependency added
- new fast distmap algorithm, up to 1000 times faster
- readImage now uses by default the native image color mode
- C functions getColorMode, getNumberOfFrames, getNumberOfChannels, getColorStrides added
- C function lib_paintFeatures renamed to paintObjects
- C function lib_matchFeatures renamed to matchObjects
- C function lib_deleteFeatures renamed to rmObjects
- C function lib_stack_objects renamed to stackObjects
- C function lib_tile_stack renamed to tile
- C function lib_untile renamed to untile
- display is faster since pixbuf are now directly built from SEXP
- writeImage now uses a quality of 100 by default
DAVIDQuery
Added maintainer name to maintainer field.
pdInfoBuilder
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/pdInfoBuilder] permanent link
pdInfoBuilder
Prep'ing to add 2nd version of db-based annotation
[/pdInfoBuilder] permanent link
SPIA
add more organisms in extdata instead of data
EBarrays
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
hopach
updated email address of author
fixed mssinitlevel to cover case where distance matrix is NULL
BicARE
Fixed some minor typos.
Fixed a typo.
arrayMvout
Standardizing reference to Artistic License 2.0.
chipseq
updates
added CpG track for mouse
EBImage
2.7.8
- validImage in C, removed isImage in C
- merged IndexedImage class within Image, no IndexedImage class anymore !
- removed spurious '...'
- classUnion ImageX instead of Image !
- now Image supports non-numeric storage.mode (e.g. logical) !
- ImageCall instead of Call to check Image validity and storage.mode
- deprecated: matchObject, stopIfNotImage
twilight
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
arrayMvout
ok
ok
ok
factor away the big data to mvoutData
all in for check
ok
get rid of bad col specs
no more affyMvout
more doc
moving towards check solution
various, covering illumina now
ok
minor changes
AnnotationDbi
added unlist2()
[/AnnotationDbi] permanent link
AffyCompatible
removed quotes from do.call
removed quotes from do.call
[/AffyCompatible] permanent link
Rintact
I have updated the man pages to incorporate a citation to the Bioinf paper
yaqcaffy
Moved geneplotter from Suggests to Depends field.
chipseq
plot improvement; allow custom peak function in diffPeakSummary
sigPathway
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
BiostringsCinterfaceDemo
added the BiostringsCinterfaceDemo package
[/BiostringsCinterfaceDemo] permanent link
preprocessCore
(1.3.6) Fix issue with non double arguements to normalize.quantiles.use.target()
[/preprocessCore] permanent link
chipseq
updates
updates
fixed a missing }
minor tweak to the man page
estimating fragment length
Rintact
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
cosmo
fixed Rd parser warnings
arrayMvout
Added missing dependency.
affypdnn
added citation
Added the mandatory vignette.
bumping up version number
Fix in "pdnn.scalevalue.exprSet"
DAVIDQuery
Added new package DAVIDQuery to Bioconductor
AffyCompatible
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/AffyCompatible] permanent link
EBImage
minor bug on abind dependency fixed
2.7.10
- fixed ReadImage bug when filename=''
2.7.9
- created tile.c, tile.h
- out of range [0:1] normalize for Magick
- matrix: channel 4, untile, getFeatures fixed
- x11 channel OK
EBImage
2.7.21
- moment features renamed from '*' to 'm.*'
- geometric hull features from 'h.*' to 'g.*' to not to be confused with Haralick's features 'h.*'
- moment features now need ref to be computed
- getFeatures now just concatenate hull, moments, edge, haralick and zernike features
- no more s2maj and s2min in hullFeatures: now only l1 and l2 (eigenvalues of the covariance matrix)(to be consistent with moments)
missed in previous commit
2.7.20
- outline renamed in ocontour, ocontour documentation added
- build warnings should disappear
pdInfoBuilder
added new template package
added new function getGeometry
start of some changes to affy ST, tiling and expression arrasy
[/pdInfoBuilder] permanent link
preprocessCore
(1.7.1)
[/preprocessCore] permanent link
dualKS
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
AnnotationDbi
Adds support to make most chip and organism sqlite files
This update adds many new functions to add functionality to make many
new kinds of organism and chip based sqlite files. In general there
is a master function for each schema that adds the ability to make
sqlite files of that type (with correct parameters). These functions
will later be wrapped in another function that should call these
functions and then also call makeAnnDbPkg() to make the sqlite file
and then wrap it up in a new package.
[/AnnotationDbi] permanent link
PLPE
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
chipseq
Update isochore mm8->mm9 mappings given corrected source data.
pdInfoBuilder
work on affy tiling and ST arrays, updated man pages
[/pdInfoBuilder] permanent link
CGHbase
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
sigPathway
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
nnNorm
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
EBImage
new in 2.7.7:
- reenumerate, hullFeatures, rmObjects, watershed: work fine on md and Color
- watershed: fixed bug when used on distmap(lena>0.5)
- getFeatures, hullFeatures, edgeProfile, edgeFeatures: work fine on md and Color
- cmoments, smoment, rmoments, moments: work fine on md and Color
- haralickFeatures, haralickMatrix, zernikeMoments: work fine on md and Color
- zernikeMoments: work fine on md and Color
- frameDist deprecated
- class.IndexedImage.R: stop message in case of TrueColor now OK
- checked all INTEGER(GET_DIM())[2] OK
- merged all features in features.R
- renamed methods-display.R in display.R, filters_watershed.cpp in watershed.cpp
- watershed is now interruptable
- objects methods moved from class.IndexedImage.R to objects.R
chipseq
more summary stats
more updates - getting into island statistics
AnnotationDbi
started a TODO list here
[/AnnotationDbi] permanent link
AnnotationDbi
Added 'drop.invalid.keys' arg to "subset" methods for Bimap and AnnDbBimap
objects (default is FALSE). Bumped version to 1.5.16
[/AnnotationDbi] permanent link
AnnotationDbi
Adds new Ensembl mappings to mammalian org packges.
Mouse, Rat and Human now can support Ensembl transcript IDs, these IDs
are availaible in new mappings and documented. The mappings for mouse
Ensembl protein IDs have also been added with this patch (previously
only MGI IDs were in place in the mouse).
[/AnnotationDbi] permanent link
EBImage
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
pdmclass
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
pathRender
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
chipseq
moved to GenomicFeatures package
metahdep
Changed biocViews entry of Statistics to Bioinformatics.
affypdnn
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
AnnotationDbi
Fix for arabidopsis custom packages.
This just fixes a bug that would prevent custom made Arabidopsis
packages from loading.
[/AnnotationDbi] permanent link
Rintact
I have updated the parser and Namespace and Desc file. The update to the parser is cosmetic (comments))
AnnotationDbi
Rollback to version 40637
Because I accidently hit ci just a little too soon...
Just a backup of major stuff I have been changing... Just in case...
[/AnnotationDbi] permanent link
chipseq
Replaced XDataFrame with DataFrame.
fix encoding
updated man page
sigPathway
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
AnnotationDbi
Modifications to Plasmodium falciparum man pages.
Corrects bugs that would otherwise be found in the Plasmodium
falciparum man pages for packages that get produced using this.
[/AnnotationDbi] permanent link
chipseq
put some more tools in context.R
BiostringsCinterfaceDemo
Following the Biostrings/IRanges split, BiostringsCinterfaceDemo now needs to depend on and to import the new IRanges package.
[/BiostringsCinterfaceDemo] permanent link
affycomp
fixed parser errors and incremented version number
chipseq
Add isochore.mm9.rda, which is isochore.mm8 mapped to mm9.
affypdnn
Replaced usage of defunct class exprSet with ExpressionSet.
MassSpecWavelet
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/MassSpecWavelet] permanent link
maanova
Removed usage (or reference) to pstricks tex style in BioC vignettes.
AnnotationDbi
Improved manual pages for makeXXXXXCHIP_DB() functions.
[/AnnotationDbi] permanent link
AffyCompatible
Update docs to new Rd parser; track changes in XML
[/AffyCompatible] permanent link
BiocCaseStudies
fixed some typos
fixed the Rd parser warnings
[/BiocCaseStudies] permanent link
PLPE
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
arrayMvout
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
AnnotationDbi
Updates to Documentation.
This updates the main vignette for AnnotationDbi with more examples,
and also updates the man pages for the homology package so that users
will in future know where the inparanoid abbreviations come from.
[/AnnotationDbi] permanent link
hopach
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
chipseq
analysis with singletons
arrayMvout
passing quickly
cosmo
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
AnnotationDbi
Fixes annotation and map counts bugs in Inparanoid packages.
This patch just repairs minor bugs in the code that generates the
inparanoid packages.
[/AnnotationDbi] permanent link
chipseq
update
updated corr
chipseq
some code using simulated data
pdInfoBuilder
Updating support for NGS Tiling Arrays - contributed by Matt Settles msettles@wsu.edu
[/pdInfoBuilder] permanent link
chipseq
update to include fibro/myo comparison
PGSEA
Secondary vignette should now build on all platforms (except windows)
EBImage
2.99.1
- starting the pre 3.0.0 release
- doc: equalize, blur, gblur, normalize, EBImage, EBImage-deprecated
affypdnn
- fixed typo in man page
- bumped version number
BiocCaseStudies
Bumping version number.
Removed matchprobes dependency.
[/BiocCaseStudies] permanent link
EBImage
merge devel with release version 3.0.1
chipseq
Fixed simulation code to handle various size read.
Changed file extension for simulated reads file.
Added information of location for simulated reads.
updating version
affycomp
Replaced data() by getData() to remove NOTES on 'no visible bindings'; Converted phenoData objects to AnnotatedDataFrame; Replaced geneNames by featureNames
Rintact
I have updated the parser so that the EBI accession codes appear the the intactHyperGraph. i have also added the complex xml file
PGSEA
Fixed a bug in the second vignette...
LMGene
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
hopach
fixed methods package declaration
BiostringsCinterfaceDemo
Following the Biostrings/IRanges split, BiostringsCinterfaceDemo now needs to depend on and to import the new IRanges package.
[/BiostringsCinterfaceDemo] permanent link
sigPathway
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
LMGene
Updated eSet objects and bumped package version numbers.
pdInfoBuilder
Fixed merging of POS and NDF files
[/pdInfoBuilder] permanent link
pdInfoBuilder
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/pdInfoBuilder] permanent link
pdInfoBuilder
Added NimbleGen Tiling Example to the vignette
[/pdInfoBuilder] permanent link
CGHbase
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
macat
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
twilight
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
chipseq
vignette fixes
updates
misc updates
updates
some doc templates
flowFP
Edited the man page for flowFPModel to indicate that a flowSet is collapsed to a flowFrame for binning.
Minor changes to the vignette to show the use of named parameters in addition to numbered parameters.
Previous change bumped version.
Fixed bug in flowPlex construction. Checks the number of instances as well as
the sample names of each instance for consistency.
Added excludeTime (default TRUE) to the model constructor so that if the user
want to consider all of the parameters in an fcs file, the constructor will
attempt to exclude the parameter containing time, if it is found.
Added 'bin_cols' to model plotting, allowing the user to supply colors to the
plotted bins, for model plotting.
Removed '<' symbol from the 'qc' and 'fancy plot color legend.
Removed references in the make system, (configure.ac) to BLAS and the gsl
library.
Removed aclocal.m4 file which is no longer needed.
chipseq
updated readAligned usage
additional peak cutoff analysis
panp
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
EBImage
Fixed ImageCall/Call bug. Now display() has a horizontal slider.
chipseq
updates
peak modeling updates
chipseq
update
pathRender
news file -- compliant?
suport for plotExG
various elements added to support plotExGraph
chipseq
added genomic introns function
new gdApply function
a few diagnostics added
lapply for GenomeData objects
chipseq
correct version of data
GeneR
fixed Rd version 2 parser warnings
macat
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
chipseq
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
BiocCaseStudies
Added functions to control output of integers in Sexprs
[/BiocCaseStudies] permanent link
SPIA
changed spia.Rd
AffyCompatible
Decrease dependency on RCurl version
[/AffyCompatible] permanent link
EBImage
Maintainer Rochade.
Now Greg maintains EBImage, Florian cellHTS2
flowFP
Added flowFP package to svn
bgx
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
AnnotationDbi
Patches bug in inpIDMapper and sqlForge_baseMapBuilder
This fixes a bug in inpIDMapper and lays groundwork for more functions
that act similarly. Also, this fixes a bug in baseMapBuilder to help
with getting the Affy annotations updated.
[/AnnotationDbi] permanent link
twilight
Removed support for soon to be defunct class exprSet.
PGSEA
Changes to vignette to support ExpressionSet class as well as updated an invalid data object.
yaqcaffy
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GraphAT
Fixed a bug related to deprecated edgemode slot of a graphNEL object.
pdInfoBuilder
Cleaning up
Fixing requirements for RMA on Exon arrays
Improved support for Affy Exon arrays
[/pdInfoBuilder] permanent link
pathRender
Removed usage (or reference) to pstricks tex style in BioC vignettes.
Rintact
Added RBGL and methods to the Depends field.
BiocCaseStudies
updated package list
[/BiocCaseStudies] permanent link
AffyCompatible
Work around XML changes
- xmlValue.XMLAttributeValue
- xmlDoc(xmlNode)
[/AffyCompatible] permanent link
AnnotationDbi
Adds support for Zebrafish and E coli.
This adds support for Zebrafish and two strains of E coli.
[/AnnotationDbi] permanent link
pdInfoBuilder
Adding structure for version 2 of pdInfoBuilder
[/pdInfoBuilder] permanent link
nnNorm
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GraphAT
Changed biocViews entry of Statistics to Bioinformatics.
chipseq
minor update
plots added
added a skeleton help page for gdApply
BiocCaseStudies
Swapped usage of old style deprecated annotation paradigm with new AnnotationDbi paradigm.
[/BiocCaseStudies] permanent link
DAVIDQuery
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
chipseq
updates to use new SHortRead filters
chipseq
starting to work on some code for chipseq work flows
AffyCompatible
Adds pkg AffyCompatible to the bioconductor repos.
[/AffyCompatible] permanent link
BiocCaseStudies
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/BiocCaseStudies] permanent link
chipseq
one more man page
added a comment
documenting some of the code
yaqcaffy
Removed unneeded geneplotter dependency.
pathRender
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
hopach
fixed methods package declaration
AffyCompatible
- make affxLicence less visible -- this licence is for the package, not
the user
- update [,.TypedAssocation,... methods for ... argument dispatch
[/AffyCompatible] permanent link
AnnotationDbi
Fixes map_counts bug for org.Sc.eg.db packages.
[/AnnotationDbi] permanent link
pathRender
better title
hopach
fixed order of commands in NAMESPACE
updated INDEX with more functions
AnnotationDbi
Added item to TODO which needs to be done in January.
Adds custom mappings capability to AnnotationDbi
This change adds a simple function for users who wish to customize
their standard annotation packages so that they can have new mappings
in addition to standard ones. Users can add extra data to their
databases, and then make mappings for this new data without modifying
AnnotationDbi.
[/AnnotationDbi] permanent link
yaqcaffy
added importFrom("graphics", "plot") in NAMESPACE
changed yaqc example dataset in vignette to speed up check
updated TODO file
incremented version number
pdInfoBuilder
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/pdInfoBuilder] permanent link
EBImage
Some work on the vignette, but there remains a lot to do.
Rintact
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
PGSEA
Added additional vignette - example PGSEA workflow
Added a minor documentation thing
BicARE
Bumping the version number and fixing the between package class links.
RmiR
Change to use RmiR.hsa instead of RmiR.db
arrayMvout
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
widgetTools
A bug that causes the wEnv function to fail was fixed
affycomp
Fixed usage of se.exprs in ExpressionSet class.
MassSpecWavelet
Update the description fields of some functions
[/MassSpecWavelet] permanent link
PGSEA
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Rintact
I have modified the depends in the DESC
I have added an deprecation message for this package as it will no longer be supported in the future.
macat
cleaned up documentation and source code
BiocCaseStudies
Updating the license reference to reflect R standards.
[/BiocCaseStudies] permanent link
AnnotationDbi
Adds missing documentation.
[/AnnotationDbi] permanent link
pdInfoBuilder
Added extra annotation for CNV probes on SNP 5/6 arrays
[/pdInfoBuilder] permanent link
twilight
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
arrayMvout
minor edit
ok
changes
for static handling of latter part of vignette
panp
Removed support for soon to be defunct class exprSet.
yaqcaffy
fixed Rd issues found by Rdversion 2 parser
fixed Rd issues found by Rdversion 2 parser
fixed Rd issues found by Rdversion 2 parser
affypdnn
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
AnnotationDbi
Moved the whole makeProbePackage() functionality (S3 methods + functions + pkg template + datasets + doc) from matchprobes to AnnotationDbi. Bumped versions: matchprobes -> 1.15.3 and AnnotationDbi -> 1.5.14
[/AnnotationDbi] permanent link
chipseq
doc updates
updates
chipseq
removed quotes from do.call
arrayMvout
passing quickly
various to pass check in time
various to speed up vignette; added method for data.frame
ok
MassSpecWavelet
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/MassSpecWavelet] permanent link
BicARE
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
chipseq
minor improvements
minor improvements
AnnotationDbi
Bug fixes for intraIDMapper
This just fixes some small bugs present in intraIDMapper. Mostly,
these have to do with the use of unlist() which is a dangerous
function to have to use.
[/AnnotationDbi] permanent link
MassSpecWavelet
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/MassSpecWavelet] permanent link
metahdep
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
SPIA
Added package SPIA to the repository
EBImage
new installation in inst/doc
PLPE
Updated eSet objects and bumped package version numbers.
LMGene
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
pdInfoBuilder
Initiated adpt to new Affymetrix format on the annotation files
[/pdInfoBuilder] permanent link
PGSEA
Fixed a bug in enforcing the size of the concepts to be tested in PGSEA()
Added "enforceRange" argument to PGSEA()
Added "grid line type" argument to smcPlot()
CGHbase
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
pdInfoBuilder
UnitTests now checks for the existence of RCMD
[/pdInfoBuilder] permanent link
hopach
Note the change to no square root transformation for distance calculations.
Note the change to no square root transformation for distance calculations. Also fixed the name of the hdist slot Call (was Method).
Note the change to no square root transformation for distance calculations. Also fixed the name of the hdist slot Call (was Method).
pdInfoBuilder
Cleaning up code
[/pdInfoBuilder] permanent link
CGHbase
Changed biocViews DNACopyNumber to CopyNumberVariants and SNPsAndGeneticVariability to SNP, GeneticVariability.
chipseq
Slight speedup of simulateReads.
Modified handling of CTCF reads and PWM-based sites.
Minor change to simulateReads verbose printing.
MassSpecWavelet
fixed a few small bugs
[/MassSpecWavelet] permanent link
PGSEA
...version bump...
chipseq
Tweaks to gene[Human|Mouse] docs.
let's bump version number every now and again
Add geneHuman.rda, hg18 analog of geneMouse.rda. The proteinID column
now has NAs instead of empty strings. Also add/revise documentation.
tried to document two more functions
added a man page for the geneMouse data
DAVIDQuery
Bumped version to 1.3.1, fixed "gene2gene" discussion in the overview/vignette, and fixed the title and author info.
pdInfoBuilder
Fixed problem on description of Affy Tiling Arrays
[/pdInfoBuilder] permanent link
maanova
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
maanova
added documentation for the matchDataToDesign param
added matchDataToDesign parameter, added code to allow the given data to be an ExpressionSet type and made some other minor modifications to the type checking code that should make it more robust to the R class system
minor comment typo
just changed EOL to unix style (no real code change)
fixed a bug in the fdr function
ignoring pdf file that gets generated in the build process
minor change to doc
minor change to tex doc
pdInfoBuilder
Fixed error in vignette compilation
[/pdInfoBuilder] permanent link
Rintact
version bump
EBImage
Added TODO.
EBImage
minor
2.99.4
- deprecated channelMix
- doc: filter2, moments, cmoments, smoments, rmoments
- doc: paintObjects, getFeatures, rgbImage, channel
2.99.3
- bwlabel OK
- safer rgbImage
adding
minor fix in documentation
2.99.2
- doc: tresh
- floodFill and fillHull : doc + test + examples
arrayMvout
various
chipseq
code for summarizing subsets
hopach
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
RLMM
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
chipseq
took out the code that reads in geneMouse, as it is now a
data set
moving more functions from the scripts into the package and
strip '*' component from aligned locations when summarizing
tidying up a few loose ends
moving functions from Scripts to R
added the island code from Scripts/islands.Rnw to the package so
we don't need to run the Rnw to get the functions
EBImage
minor
winlibs deleted
1) Windows DLL deleted. Should compile on Bioconductor gewurz Windows building machine providing that the 2 environment variables:
- IM_BASEPATH points to the ImageMagick directory
- GTK_BASEPATH points to the GTK directory
2) Now compile on R-2.8.0 since the R_tcldo() hack has been removed. The RGtk2 mechanism is now used to pool the Gtk events from R.
chipseq
new functions and more stuff in the use case document - in particular
an example of peak subtraction
RpsiXML
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
xcms
Standardised peak area calculation by introducing scan-distance multiplier to findPeaks.centWave()
Biostrings
Reworked the core constructors BString(), BStringList() and families: better semantic (via the new start and nchar args), better speed (on character input for now, other type of input will follow) and better internal code. Time to bump.
RpsiXML
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
keggorth
fix graph with update; change to .db environment
RpsiXML
This fixes a small bug in hyperGraphSpeciesConverter
This allows the hyperGraphSpeciesConverter() to return a hypergraph
when you started with a hypergraph.
Biostrings
Added more genomes to phage data set and composed examples using them.
xcms
added missing closing bracket
graph
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xcms
fillPeaks/getPeaks: fixed problem with nonexisting retention times due to retcor(),
fill in zero instead of NaN (which breaks diffreport), but print a warning
xcms
Removed unnecessary use of data.frame in findPeaks.centWave(), this fixes
a long delay when large peaklists are generated
xcms
Fixed return value of group(method=nearest) to be a proper (grouped) xcmsSet
BCRANK
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
ctc
Replaced reference to soon to be defunct exprSet class with ExpressionSet.
CoCiteStats
fixed Rd parser warnings
aroma.tcga
Create aroma.tcga
RpsiXML
Release 1.5.16: internal handlers are almost complete until some exceptions. No public API is changed. See NEWS for information
xcms
Fixed image(xcmsRaw)
Added xcmsRaw CDF export contributed by Peter.Watkins
Now really commit 1.11.18 as 1.13.1
RpsiXML
Support update: The package now supports CORUM database from MIPS
xcms
Extended FTICR Vignette
Preparing for BioC 2.2 release
Added TandemMS and MSn vignette
Vignette for FTICR picking and Alignment
GGBase
some basics
Biostrings
Add more information to PairwiseAlignmentSummary show output.
Minor change to mismatchSummary function.
Created a PairwiseAlignmentSummary class to make it easier for users to get summaries of fitted pairwise alignments.
Added nmatch and nindel functions.
Added a weight argument to mismatchSummary function.
Minor change to man page.
Minor speedup to mismatchSummary method for PairwiseAlignment objects.
Biostrings
Small improvements to XStringSet basic capabilities:
- added "width" and "narrow" methods for character vectors;
- added "threebands" method for character and XStringSet objects;
- improved XStringSet-class.Rd man page;
- modified PDict() constructor to use "threebands" (for XStringSet)
internally for splitting the input dict into head+tb+tail parts.
Bumped version to 2.11.28
limmaGUI
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
preprocessCore
(1.1.9) Commit missing c source files. This should allow preprocessCore to successfully build and also pass R CMD check (which it has not done since 1.1.6)
[/preprocessCore] permanent link
HEM
Changed biocViews entry of Statistics to Bioinformatics.
affxparser
Version: 1.15.5 [2009-02-14]
o Fixed a bug related to SET_VECTOR_ELT/SET_ELEMENR used on strings.
Affected readChp.
o Fixed a bug related to naming of the list structures (we assigned
a list instead of a character as the name. Affected readCdfUnits and
readCdfCellIndices.
o Updated Fusion from 1.11 to 1.12.
o Fixed a bug in the example for readCdfUnitsWriteMap: the package
AffymetrixDataTestFiles was misspelled, so the tests were never run.
siggenes
Added a class denspr so that the output of denspr can be plotted easier.
VanillaICE
fixed problem with findBreaks function -- removed rows with multiple chromosomes
Biostrings
Minor code change to use accessor function in internal code.
Biostrings
Bumped version to 2.13.22 in order to release the new code for fast matching of the head/tail of a PDict object. In some situations where the head/tail is very narrow (<= 8b in total), the overall speed up for matchPDict() can be 10x or more.
Biostrings
added some references to the man pages for PDict/matchPDict
Biostrings
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Added "width" method for MIndex objects.
Renamed ByName_MIndex class -> SparseMIndex and completely turned off
any code related to this class (the SparseMIndex class is not used
anymore, but might be needed again in the future). As a side effect,
'R CMD check' is now totally happy.
Fixed bug in consensusMatrix() when some of the values passed thru the 'shift' arg were <= - 'width'.
small improvement to man/nucleotideFrequency.Rd
Biostrings
Added another condition for a valid alignment.
affxparser
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
graph
supressing warnings when setting graph.pars because we do explicit checking anyways.
Biostrings
fixed a typo
added transcribe and cDNA as functions
that were missing
HilbertCurveDisplay
corrected setting of PKG_CONFIG_PATH
(use :=, not =, and ;, not :)
added README for standalone dir
changes Makevars.win to set pkg-config path
added Makefile for stand-alone interface
[/HilbertCurveDisplay] permanent link
flowClust
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
RpsiXML
methodDefs also renamed into AllMethods.R
Release 1.5.9, codename 'Amsterdam's Morning': filenames further follows convention; Makefile is added to simply package management; First refactoring of NAMESPACE is done with specifying imported classes and methods
version 1.5.8: Code name 'Amsterdam's Dawn': classes supporting ALL PSI-MI 2.5 specifications have been added to prepare for a major update
Biostrings
Speed up "countIndex" method for MIndex objects (by using new
"elementLengths" method for list objects).
Bumped version to 2.13.14
Agi4x44PreProcess
NAMESPACE:version 1.3.3
in BGandNorm, we pass the matrix MMM=RGlist$G - RGlist$Gb to the backgroundCorrect(...,normexp) function, so that only the 'green' color is computed. Internally, the backgroundCorrect(...,normexp) corrects the green and red channels if we pass an RGList. By default, the function fit a normal+exponential convolution model to a vector of background corrected intensities (RGList$G - RGList$Gb), that's why we define MMM=RGlist$G - RGlist$Gb. We specify the background signal used by backgroundCorrect() in the BGandNorm()function using the argument background
[/Agi4x44PreProcess] permanent link
Biostrings
Renamed consmat consensusMatrix and deprecated consmat.
Added a baseOnly argument to the consmat method for PairwiseAlignment objects.
Removing the consmat method for AlignedXStringSet objects since it makes little sense.
Optimized performace of consmat function.
xcms
Fixing typo in profBinLinBase
BGmix
added BGmix package
Agi4x44PreProcess
fixed the parser warnings and made the man page more readable
[/Agi4x44PreProcess] permanent link
Biostrings
Replaced notion of inserts with indels in pairwiseAlignments since this information represents either insertions or deletions.
annotate
Updated NAMESPACE and DESCRIPTION.
xcms
Fixed gcc compiler Warning
CoCiteStats
Changed biocViews entry of Statistics to Bioinformatics.
Biostrings
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.
Biostrings
Minor changes to function descriptions.
Add creation of PairwiseAlignment from strings to the examples section.
Biostrings
Sped up computation in pairwise alignment by better approach to allocate memory.
Revered back to using R_alloc in pairwise alignment functionality.
I removed the now irrelevant old email: "WolfgangUseCase.txt".
I removed the capricious use "pstricks.sty" in the vignette.
Minor edits to Alignment vignette to get it into "release" quality.
Biostrings
Fixed serious bug in vcountPDict(): except for the 1st column of the returned matrix (where all match counts seem to have been correctly reported), in all other columns the match count for any duplicated pattern was always reported to be 0. Bumped version to 2.11.29
Biostrings
Changing pairwiseAlignment's gapExtension default value to -2.
Modified calculation of profile to mean start of alignment rather than first substitution.
Biostrings
Fixed the traceback when insertions are immediately followed by a deletion and vice versa in pairwiseAlignment.
nem
Version bump.
siggenes
Just some clean ups.
Some new features for annotating SNPs in html output.
ppiStats
Revised the dependencies to have a smaller search patch footprint.
Biostrings
Reduced size of data used with vcountPDict() in matchprobes.Rnw vignette so it has a chance to work on Windows too. In the same vignette, use CL2001032020AA.cel now in affydata (added in >= 1.11.4) instead of the one found in (deprecated) matchprobes package. Fixed typo in matchPWM.Rd. Bumped version to 2.11.32
Biostrings
matchPWM(): When passed a Position Weight Matrix of doubles, matchPWM()
doesn't coerce it to an integer matrix anymore. The same apply to its
'min.score' argument. PWMscoreStartingAt() now always returns a vector
of doubles, whatever the storage mode of the PWM was (this could be
Bumped version to 2.13.1
Biostrings
Added safe (and user-friendly) "IRanges" and "Mask" constructors. Reworked the examples in MaskedXString-class.Rd. Some other samll fixes and improvements.
Deprecated the needwunsQS function and added more information in the Alignments.Rnw vignette on optimal pairwise alignments.
Fixed some problems with the "names<-" method for IRanges object. Added "names<-" method for MaskCollection objects. Bumped version to 2.7.54
Fixed latex issue.
Clarified what quality1 and quality2 arguments represent.
GLAD
impl?\195?\169mentation en C de findCluter
sauvergarde
Biostrings
put back fastaEx from Biostrings1
Renamed Exfiles/ folder as extdata/. No version bump.
DEDS
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Biostrings
sync up with the RELEASE_2_3 branch
preprocessCore
(1.3.4) Fix memory leak in determine_target (on pthreads enabled machines)
[/preprocessCore] permanent link
BGmix
should work on Windows now
ontoTools
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Biostrings
Modified replaceLetterAt() example.
Some improvements to replaceLetterAt():
- added support for logical or Rle 'at' argument in "replaceLetterAt"
method for DNAString objects;
- added a "replaceLetterAt" method for DNAStringSet objects (with the
current restrictions that 'x' and 'at' must be rectangular i.e. 'x'
must have a constant width and 'at' must be a logical matrix with
the same dimensions as 'x').
Bumped version to 2.13.8
Fixed coverage method for PairwiseAlignedFixedSubjectSummary objects.
GGBase
plot_EvG2
annotate
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
VanillaICE
export genotypeEmissionCrlmm
GGBase
phenoVar in
GeneSelector
fixed Rd version 2 parser warnings
[/GeneSelector] permanent link
flowClust
small fix: rectify the problem of not transforming the mu estimates in getEstimates() and the plotting methods when lambda is 1.
Biostrings
Fixed bug causing XStringViews_match_TBdna() to report wrong match ending positions for duplicated patterns. Bumped version to 2.9.16
RpsiXML
Release 1.5.10. Code name 'Amsterdam noon'. 'typedList' class and public constructor added. Other file changes. Check 'NEWS' released along the package for update details. JDZ
add constructuor and how methods for typedList.
annotate
Modifications to allow end users to add arbitrary repositories for use with the htmlpage() function.
ctc
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
preprocessCore
(1.3.3) Fix memory leak in use_target
[/preprocessCore] permanent link
annotate
Modifications to make PWAmat() work with new pkgs
Changes were to PWAmat() and enable it to get an incidence matrix for
the newer organism based annotations as well as the older chip based
packages. Changes primarily are to allow PWAmat() to know when it has
an organism based package or chip based package so it can return the
correct result.
annotate
Added allValidKeys function.
The allValidKeys function returns all the valid primary IDs for an
annoation package.
affxparser
Robert adding in the necessary files to Makevars for reading CHP files
GGBase
use snpMatrix 1.7 API
maSigPro
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
Biostrings
Finished adding code to support the endGap argument to pairwiseAlignment.
affxparser
Version: 1.13.4 [2008-08-05]
o Renamed the HISTORY file to NEWS.
o Now help(createCel) (and its example) clarifies that
the template CEL header can be of v3 (ASCII),
v4 (binary;XDA), or v1 (binary;Calvin).
VanillaICE
improved checks in viterbi
annotate
Long overdue update to the useDataPkgs vignette.
TypeInfo
Update docs to new Rd parser
BCRANK
bug fix for R 2.8
xcms
fixed docu mismatch for score_fun
Biostrings
Minor typo fixes.
finished to resync code with new XInteger class definition
bumped version to 2.9.72
xcms
Fixes for Pipeline stuff
Fixed mzClust Pipeline
added Class for handling of Tandem MS / MS^n
DEDS
Removed usage (or reference) to pstricks tex style in BioC vignettes.
Biostrings
Added codes, codec, enc_lkup, and dec_lkup methods for XStringSet classes.
Minor change in terminology from match to align in code.
Added "matchPDict" methods for XStringViews and MaskedXString objects (only for a DNA input sequence). Version bumped to 2.9.10
Biostrings
Added the countPDict() function: faster than matchPDict() if getting the
number of matches is what matters only (without regarding their positions),
especially when there is a high number of matches.
Version bump.
Biostrings
updating the consmat manual page
adding the FASTA files for two yeast genes
Added "as.character" and "consmat" methods for "BStringAlign" objects. No version bump.
Version finally bumped after a series of changes:
o matchPattern.Rnw vignette replaced by much improved GenomeSearching.Rnw
vignette (still a work-in-progress).
o reverse(), complement() and reverseComplement() now preserve desc(x) when
applied to BStringViews object x.
o matchPDict() now returns a PDictMatches object (new class) instead of a list
of integer vectors. The user can then subset this PDictMatches object with [[,
convert it into a list of integer vectors with as.list, or convert it into a
set of views on the original subject with extractMatches(). Other functions
can (and will) be added later in order to provide a wider choice of
efficient conversion/extraction tools.
WARNING: This is still a work-in-progress. Function names and semantics are
not yet stabilized!
gaggle
fixed bug with matrix naming before broadcast
preprocessCore
(1.5.2) normalize.quantiles.determine.target() and normalize.quantiles.use.target() now have a "subset" argument
[/preprocessCore] permanent link
VanillaICE
numerous changes to plotting methods (getPar). Added the featureData slot to the class defintion of HmmPredict, as well as a few more accessors
keggorth
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Biostrings
More work on the PDict() constructor (changed its signature, the length of the Trusted Dictionary must now be specified via the 'tb.width' arg instead of the 'tb.end' arg). Version bumped to 2.7.23.
preprocessCore
(1.1.5) The subColSummarize* functions now return a matrix with rownames. Now it is clear which rows of the resulting summary matrix correspond to which values of the group.labels variable. This helps clarify the previous situation where it done alphabetically.
[/preprocessCore] permanent link
Biostrings
Don't use the ByName_MIndex class anymore (will be removed soon). MIndex objects returned by matchPDict() (and family) are now always of subtype ByPos_MIndex (used to be ByName_MIndex if the 'pdict' arg had names).
VanillaICE
do not evaluate code chunk 5 in illumina howto vignette
syslibGTK
Fixed some typos and inserted FIXMEs.
Biostrings
Added sample data sets to illustrate use of pairwiseAlignment on a small sample of short reads from a Solexa machine.
Switch memory allocation from R_alloc() to malloc()/free() in pairwiseAlignment to speed up calculations by avoiding swapping.
Fixed two bugs in mismatchSummary for QualityAlignedXStringSet objects:
1) Corrected integer overflow issue.
2) Corrected output when qualityType == "Solexa".
Optimized performance for pairwiseAlignment when scoreOnly = TRUE and gapOpening = 0.
Added more information to the vignette introduction.
Biostrings
Added some more parameter checks to stringDist and cleaned up its man page.
Updated STRING ALIGNMENT section of the NEWS file to reflect changes since last release.
Changed stringDist argument ignore.case to ignoreCase.
Added another set of examples to the stringDist man page.
Added a stringDist function to Biostrings.
Biostrings
Added "unlist" method for XStringSet objects.
- Added "subseq" and "subseq<-" methods for character vectors and
XStringSet objects.
- Bumped version to 2.13.7
Updated dependents of IRanges to reflect changes in List/ListLike classes.
SMAP
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affxparser
CPP code for parsing CHP tiling arrays
code of the parsing chp files
xcms
fixed tex math in manpage
GGBase
Changed biocViews entry of Statistics to Bioinformatics.
siggenes
Added a class denspr so that the output of denspr can be plotted easier.
Biostrings
Use closest integer mismatch in trimLRPatterns when mismatch parameter is in (0,1).
annotate
Small changes to the htmlpage() help page to hopefully make things less opaque.
ppiStats
i have updated the estimateCCMErrors function
Biostrings
Re-aligned the XStringViews code with latest changes in the Views code (from the IRanges package). Got rid of recently added "Views", "substr" and "substring" methods for MaskedXString objects: these were deliberately omitted so far because there are other possible and reasonable interpretations of what they could mean, so let's just hold on for now (besides, these new methods were not documented). Added "order" generic with a method for XStringSet objects (dispatch on "..." is only supported starting with R 2.8.0). Bumped version to 2.9.71
flowClust
initialization using random partitioning
Biostrings
Adding more information to the matchLRPatterns and trimLRPatterns man page.
Reverting change to trimLRPatterns to not round when mismatch value in (0,1).
Biostrings
Added support for logical vectors when subsetting PairwiseAlignment and AlignedXStringSet objects.
Slight refactor to mismatch method for PairwiseAlignment object to improve performance.
Fixed a bug in mismatch method for objects of class PairwiseAlignment.
GeneSelector
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/GeneSelector] permanent link
Biostrings
[merge -r 32724:32884 from the testing branch of Biostrings]
This merge includes:
o Addition of the 'dups0' slot to the ByPos_MIndex class: this allows a more
compact representation in memory of a ByPos_MIndex object that holds the
hits of a set of patterns that has a lot of duplicates. The benefit is
really noticeable when the patterns that are highly represented in the
original dictionary have a lot of hits which seems to be typically the
case when matching Solexa data against their reference genome. In this
case, using the new 'dups0' slot can make the ByPos_MIndex object about 3
times smaller.
o Take advantage of this new 'dups0' slot to improve the way duplicated
patterns are handle thru the "PDict -> matchPDict() -> MIndex" pipe. The
new strategy is to "remove them as early as possible and put them back as
late as possible". This leads to a gain in speed and also less memory is
needed to store the hits in the temporary buffer.
o Added a set of "coerce" methods for turning an arbitrary XStringSet object
into a BStringSet, DNAStringSet, RNAStringSet or AAStringSet instance (via
the as() function).
o Some internal rework of the BStringSet(), DNAStringSet(), RNAStringSet()
and AAStringSet() constructors (just cleaner code, no new feature).
o Added an "append" method for XStringSet objects. An important use case for
this is to put together a set of short reads and their reverse complements
in a single DNAStringSet object and then to turn this object into a single
PDict object (dual PDict object). Then this dual PDict object can be used
to walk each reference sequence only once (instead of twice) in order to
get the hits in both strands (+ and -).
o A couple of small corrections to the matchPDict() man pages.
Version bumped to 2.9.59
Added nucleotideSubstitutionMatrix function.
maskMotif(x, motif) now does not mask again what's already actively masked
Moved the MaskCollection class, its methods and the mask importation utilities (read.agpMask(), read.gapMask(), read.liftMask(), read.rmMask() and read.trfMask() functions) from this package to the IRanges package. Bumped version to 2.9.58
xcms
Fixed Documentation
BCRANK
Updated references and contact info
Updated references and contact info
affxparser
Added the feature of reading the DAT header of CEL files
HilbertCurveDisplay
minor change to source code comments
changes to allow for compilation under Windows
[/HilbertCurveDisplay] permanent link
xcms
Fix another windows build issue
Added findPeaksMPI() MPI slave function
xcms
Fixed warnings in Obiwarp with cor_opt
GGBase
mods to featureFilter to kill the hap and qbl chroms
ok
minor fixes
new filters and doc
fixup
GGBase
trying to pass chk
flowClust
Changed unprintable character to '.
flowClust
update getEstimates(); includes an approximate variance estimate
Biostrings
Fixed the description of the max.Rmismatch argument to the trimLRpatterns function.
xcms
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
graph
Fixed DLL registration. Broken when changed name to DLL to remove conflict with graphviz.
ontoTools
fix warning on grep method
annotate
some stuff for pubmed-based literature page generation
miRNApath
Changed biocViews entry of Statistics to Bioinformatics.
preprocessCore
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/preprocessCore] permanent link
VanillaICE
changed one line in vignette
added copyNumber.scale option. needs to be a standard deviation on the appropriate scale
affxparser
Version: 1.15.6 [2009-02-20]
o Added optional argument 'newChipType' to convertCel() for overriding
the default chip type. Useful for updating the formal chip type
of old CEL files.
o Removed all gc() calls in convertCel().
DynDoc
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
RPA
Standardize license
Biostrings
- Default preprocessing algo is now "ACtree2" instead of "ACtree"
(support for 'fixed=FALSE' in ACtree2 is currently broken and
will be fixed ASAP).
- Renamed PDict() argument 'type' -> 'algorithm'.
- Bumped version to 2.11.42.
Improved the ACtree2 container to support Aho-Corasick trees with more nodes. The new limit is 2^32-1 nodes i.e. 4x the previous limit of 2^30. This should allow the preprocessing of dictionaries made of about 200 millions unique 35-mers on a system with enough memory (64 GB in that case). ACtree2 still needs more testing before it can replace the old ACtree container (the current default, limit = 2^28 nodes).
BCRANK
Text is flushed to console
Biostrings
added uniqueLetters() and use it internally to avoid code duplication
Minor tweaks in inequalities during traceback of pairwise alignment.
Added a bit more documentation for ambiguityMatrix argument.
Added support for ambiguity mappings in quality-based pairwise alignments.
Minor variable renaming.
Fixed title in man page.
Added capability to support ambiguity letters in quality-based pairwise alignments.
Fixed formula in man page.
Biostrings
Added N50 doc from Nicolas Delhomme (with some small tweaks). Bumped version to 2.13.24
flowClust
modified namespace - not to import the curv2filter, curv1filter and quadGate classes from flowCore for compatibility with previous versions of flowCore
modified namespace - import only relevant classes and methods instead of the whole namespace from flowCore
siggenes
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
xcms
fillPeaks/getPeaks: fixed bug introduced with 1.17.9's bugfix, that filled in zero intensities
graph
fixing bug in cobineNodes
fixing a bug in edgeWeights when there are no edges defined
SLGI
Added open = "rt" to gzfile function call to get man page example to run on Windows.
Biostrings
DNAStringSet() and PDict() now support direct "probetable" input (e.g. DNAStringSet(drosophila2probe)) for convenience.
Added support for min.mismatch argument in matchPattern() and family.
Completed support for min.mismatch argument in matchPDict() and family. Bumped version to 2.13.32
Biostrings
Temporarily reverting back to r40103.
Refactored the match reporting facilities used by matchPDict() at the
C level: code is now simpler and cleaner (no more global variable).
Bumped version to 2.13.18
Improving on dinucleotideFrequencyTest output.
Adding Monte Carlo simulations to dinucleotideFrequencyTest.
Removing unneeded variables for pairwise alignment C code.
gaggle
fix bug where boss would not autostart
affylmGUI
changes on dashes to ordinary ones
limmaGUI
Removed whitespaces from Rd files containing /items{stuff} {
VanillaICE
Added Biobase to the Depends field.
GeneSelector
Added the GeneSelector Package to bioconductor.
[/GeneSelector] permanent link
xcms
Debugging output for Mac Quartz problem
Fixed xcmsBoxPlot(). Bumped version to 1.13.11
dyebias
version 1.3.3; see ChangeLog for details. Brought up-to-date with upstream (i.e. UMCU) revision 3710.
PAnnBuilder
Added package PAnnBuilder to the repo
Biostrings
Minor corrections to vignette.
Agi4x44PreProcess
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/Agi4x44PreProcess] permanent link
GGBase
various steps towards renovation
dropping the sqlite approach to snp locations
[/preprocessCore] permanent link
Biostrings
Reworked the findPalindromes() API:
- change in terminology to align with established practices: "antipalindromes"
are now called "complemented palindromes" and "the gap" between the 2 arms
is now called "the loop";
- no more 'anti' arg: use findComplementedPalindromes() to find complemented
palindromes;
- the 'max.ngaps' arg has been renamed 'max.looplength';
- there is a new 'min.looplength' arg (not yet supported);
- there is a new 'max.mismatch' arg (not yet supported);
See ?findPalindromes for more details.
Biostrings
Fixed a bug in duplicated method for XStringSet objects when length = 1.
Fixed vignette usepackage issue on Windows.
Switched to using binary search in %in% and match methods for XStringSet objects.
Allow for single numeric nomatch arg, which will be converted to integer, to match method for XStringSet objects.
Biostrings
Fixed xlab in exercise plot.
Removed usage (or reference) to pstricks tex style in BioC vignettes.
Change to show method for AlignedXStringSet objects.
xcms
Added plotting for direct infusion spectra in diffreport()
Fix fillPeaks.MSW(), add filled flag for peaks in xcmsSet
syslibGTK
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
hypergraph
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
ontoTools
updated serialized graph objects
Biostrings
improved man/translate.Rd
- Added the codons() and translate() generic functions with methods for
DNAString, RNAString, DNAStringSet, RNAStringSet, MaskedDNAString and
MaskedRNAString objects.
- Added missing documentation for transcribe(), cDNA(), dna2rna() and
rna2dna().
- Bumped version to 2.11.4
sync up with trunk
Biostrings
Added "chartr" method for XStringSet and BStringViews objects. Some small changes and additions to the C interface. Bumped version to 2.7.39.
VanillaICE
Added processed data object. Added inst/testing directory. Copy number should always be stored on the original scale
Biostrings
Fixed a bug when you only have a single letter in the alphabet for quality-scaled pairwiseAlignments.
Fixed a bug in mismatchTable when there are no mismatches.
Added simple implementations of set operations for XStringSet objects.
Changing the vignette index entry.
BGmix
Removed usage (or reference) to pstricks tex style in BioC vignettes.
xcms
Fix a few bugs in the pipeline framework. Add profileMatrix<- for
setting a pre-generated profile matrix on an xcmsRaw.
GGBase
minor changes, omit chromInds
GGBase
error handling improved
conditions code improved
VanillaICE
pass beta argument in the initialize method for HmmParameter to the initialize method for HmmOptions
bug fix in the initialize methods. length(beta) is 1 if not specified
if emission probabilities is supplied to the initialize method for HmmParameter, several options in the HmmOptions class can be skipped...
xcms
Add targets all: and .PHONEY: to Makevars, to both build and clean
source
preprocessCore
(1.3.4) Fix memory leak in determine_target (on pthreads enabled machines)
(1.3.3) Fix memory leak in use_target
[/preprocessCore] permanent link
pcaMethods
Fixed warnings and notes
Biostrings
Added the maskMotif() generic function for masking a sequence by content.
As a consequence, previous 'masks(x) <- "motif"' syntax must be replaced by
new 'x <- maskMotif(x, "motif")' syntax.
Bumped version to 2.9.3
VanillaICE
updated a few of the man pages
affxparser
Last commit contained an embarrassing bug. Fixed
Fixed the loading of R.utils in findFiles. This loading had bad consequences for R CMD check - unfortunately. A better fix would be to take care of the problem at its root.
pcaMethods
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xcms
Code cleanup in obiwarp
ppiStats
I have update the namespace and desc
GGBase
minor changes: internal longnsubset, coercion
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
xcms
Fixed small NA bug and started score_fun methods choice. Currently commented out.
Added back 'overlay' function which was deleted?
Biostrings
Added matchPWM and countPWM methods for XStringViews and MaskedDNAString objects.
RpsiXML
Changelog update: Version 0.0.6 is added to bioc-devel
GGBase
Removed usage (or reference) to pstricks tex style in BioC vignettes.
RpsiXML
Version bumping: V0.0.5, verbose mode added
Changes needed by verbose mode
Function extension: high level parsers added verbose mode: parsing state can be displayed
changlog
Biostrings
Minor documentation changes.
xcms
Wiki Markup
Fixed an off-by-one bug in group.mzClust
VanillaICE
added confidence scores for crlmm on affy 6.0 platform to data subdir. Added function for computing emission probabilities on crlmm genotype calls that uses the confidence scores -- currently undocumented (genotypeEmissionCrlmm)
xcms
initialise variables gcc complained about
fix error in searchMetlin method.
xcmsRaw collect changes for simple-er code
Added man page for searchMetlin
GLAD
version 2.2.5
Biostrings
Added hasLetterAt() (see ?hasLetterAt).
nem
Fixes
Biostrings
"Views" method for MaskedXString objects won't warn that "masks
were dropped" anymore if none of the masks in subject is active.
Minor changes to Rmpi usage for pairwiseAlignment to minimize data copying to and from slave nodes.
Adding Rmpi-enabled pairwiseAlignment fits.
Removing generic specification of score and order since they are now defined in IRanges.
xcms
docu fix
Biostrings
Another change to the CWdna_PDict class (the @dups slot is back, the SparseList are gone, @dups is now of type Dups and is twice bigger than the old @dups) in order to fix PDict() performance issue when the input dictionary contains highly repetitive reads. Version bumped to 2.9.18
Biostrings
cleaned Depends field
gaggle
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
rbsurv
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Rdbi
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowClust
adding a summarizeFilter method in order to collect the information from the filterResult
BCRANK
Allowing IUPAC nucleotide symbols in fasta file. New text and seqLogo example in vignette.
affxparser
o (unexposed) function .pgfProbeIndexFromProbesetIndex failed to
handle last probe correctly
Biostrings
Fixed a dash in man page.
Fixed a dash in man page.
Minor man page edit.
Added some documentation on ambiguityMatrix for pairwiseAlignment.
GGBase
call reflectance
biocGraph
Conditional added to check for running on Windows.
Cleaned up dependencies by removing Biobase from depends and XML from suggests and placing geneplotter in imports. Also make the biocGraph vignette friendly for Windows building.
xcms
Changed the determination of mz boundaries in fillPeaks, added comment on NaN and zero values to manpage
Biostrings
Added next_XStringSet_elt_asRoSeq() to the C interface and use it in C function XStringSet_char_frequency() to speedup "alphabetFrequency" methods for XStringSet objects (4x speedup). Bumped version to 2.7.38.
more small improvements to alphabetFrequency() based on Martin's feedback
small improvements to alphabetFrequency() based on Martin's feedback
[again] The additional 15x speedup for alphabetFrequency() on XStringSet objects when 'collapse' is TRUE turned out to be broken. Removed it.
No, the additional 15x speedup for alphabetFrequency() on XStringSet objects when collap
Fixed small problem in alphabetFrequency() when 'freq' is TRUE.
Polishing alphabetFrequency() for an additional speedup of 15x on XStringSet objects when 'collapse' is TRUE.
Reworked alphabetFrequency() (most of it is now done in C). The new implementation is > 250x faster on XStringSet objects.
Biostrings
Made readFASTA() quiet on Noah Hoffman's suggestion. Bumped version to 2.11.9
nem
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
siggenes
Changed biocViews entry of Statistics to Bioinformatics.
Biostrings
added doc alias for Expanded_TB_PDict
XStringSetList now contains IPartitioning
added stub for man/XStringSetList-class.Rd
Added some basic operations on XStringSetList objects (not intended to be a full featured class for now).
Added the XStringSetList (virtual), BStringSetList, DNAStringSetList, RNAStringSetList, AAStringSetList and Expanded_TB_PDict classes. No methods yet.
xcms
fix another uninitialised int i
Biostrings
Updated the Depends and Suggests fields and changed the license from LGPL to Artistic-2.0.
Renamed IntIntervals class -> IRanges. Version bumped to 2.7.31
RpsiXML
DIP label changed into DIP
version bumping: support extracting interaction type from either shortLabel or full name
confidenceValue generic added
interaction type update: in case 'shortLabel' does not exit, the 'fullName' element will be used to extract interaction type
graph
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
flowClust
bulk update; version 2.0
ppiStats
I have added the man page for the following function
I have updated the code for the new function
GeneSelector
Changed biocViews entry of Statistics to Bioinformatics.
[/GeneSelector] permanent link
Biostrings
turned off runit-matchDNAPattern.R and fixed runit-XString.R and runit-matchPDict.R
moving unit tests (again) from tests/UnitTests to inst/UnitTests -- much better :)
moving unit tests from inst/tests to tests/UnitTests
Bug fixes:
- Fixed problem reported by Hector Corrada Bravo where PDict() would
fail on a constant width dictionary containing IUPAC ambiguity letters
even if the specified Trusted Band didn't contain any ambiguity.
- A long due fix: made "startIndex", "[[" and "unlist" methods work
properly on any MIndex object (used to be broken when the MIndex
object was the result of using matchPDict() on a PDict object with
a Trusted Band not covering the entire dictionary).
- Updated and improved man/matchPDict-inexact.Rd
- Bumped version to 2.11.8
Added a degap argument to the aligned method for PairwiseAlignment objects.
Minor edits to alignments vignette.
flowClust
setMethods.R - put back default value in the replacement function
namespace - quotation marks removed
flowClust.c - comment out R_init_flowClust
setMethods.R - remove default value in the replacement function
all for testing only
Biostrings
Added the read.agpMask() function for extracting a mask from an NCBI "agp" file. Version bumped to 2.9.9
Adding an external vector class for numeric data.
Fixed the .valid.XStringAlign function.
Implemented fast "as.character" methods for XStringSet and XStringViews objects. Other minor internal improvements. Version bumped to 2.9.8.
miRNApath
Fixed changes in runEnrichment, added PDF file with Alzheimers data views.
RpsiXML
Release 1.5.13: Some handlers are added, more to be implemented. No public user API is affected yet. JDZ
Release 1.5.12: Constructors and accessors are added for most of the XML elements. User API are not affected in the release. JDZ
Relase 1.5.11: internal structure updates and no user interface is affected. See the NEWS file released along for details.
ppiStats
I have updated the depends and imports in the DESC and NS; still needs work
Biostrings
missed on place
affxparser
Add necessary headers to Windows Makefile
Biostrings
Added indel, insertion, and deletion methods for PairwiseAlignedXStringSet objects.
HilbertCurveDisplay
Fixed a minor typo.
[/HilbertCurveDisplay] permanent link
xcms
added citations
Added group.nearest() and cleanup of src/ramp.cpp for gcc-4.3
flowClust
option for gaussian mixture model
make existing methods adapt to gaussian mixture model
fix minor bugs in density plots
update man pages to reflect recent additions/changes
update getEstimates; includes an approximate variance estimate
preprocessCore
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/preprocessCore] permanent link
xcms
fixes for and in xcmsMSn vignette and documentation
added missing xcmsProtoFilterProfile
Merged manpages, removed illegal filename
added METLIN XML reader URL:metlin.scripps.edu/download/MS.XML\nAdded basic ppm and ppmDev\nAdded array matching
Biostrings
Added the N50() function from Nicolas Delhomme. Bumped version to 2.13.21
GLAD
Changed biocViews DNACopyNumber to CopyNumberVariants and SNPsAndGeneticVariability to SNP, GeneticVariability.
flowClust
add criterion()
bumped version number
Biostrings
Better fix for adjacentViews.
Fixed a bug in adjacentViews to allow the handling of character vectors.
maSigPro
fixed Rdvision 2 parser warnings
GeneSelector
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/GeneSelector] permanent link
GGBase
minor change to allow rsid subsetting on smlSet
xcms
Reapplied Colins Fix + Michaels changes
enable write.cdf()
Backported mzClust stuff
VanillaICE
updated man page for Pi
Added alias for Pi method for HmmParameter objects to Pi man page.
xcms
Removed duplicate alias in split manpage
Added an xcmsPeaks class, an instance of which is returned by each
findPeaks method. Changed a warning; return(NULL) in one function to a stop.
fixed selection of polarity in xcmsSet
xcmsGUI
This just creates an empty project for xcmsGUI
graph
bumped version number
added defunct graph object for test purposes
xcms
boxplots made in wrong order due to pvalue sorting FIXED
updated to reflect changes in code for mult-group analysis
added boxplots for multiple groups and anova stat's
findPeaks.centWave: save some time: compute dppm only if needed
RpsiXML
version bumping: graph functions to part refactored, documentation updated
export validation function
documentation update
problem with stopifnot solved
numInteractors and numInteractions added, wrappers for counting
error-option in psimi25XML2graph removed
RpsiXML vignette
Rnw file depends on the style file
psimi25XML2Graph refactored. First step: interactionEntry refactored to interactionEntry2graph
affxparser
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
xcms
Fix windows build
major speed improvement in group(nearest)
DEDS
removed quotes from do.call
xcms
Remove tabs and inserted space as per bioconductor rules :)
RpsiXML
I have modified the parsing code to add the exact phrase "two hybrid" as a search criterion and version bump
ppiStats
I have fixed a typo in the code which created a bug
PAnnBuilder
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GGBase
now the CEU snp locations are in GGBase
inits for netCDF
fixup
fixup
Biostrings
Reworked the class hierarchy:
- Added the .IRanges class (not exported): now the IRanges class is just
the exported version of the .IRanges class (it derives directly from
it without any additional slot). Replacement methods "start<-",
"end<-" and "width<-" are only defined for IRanges objects so the user
cannot use them to modify a .IRanges object. Therefore the "safe" .IRanges
class can be used to make the BStringSet class (and family) "safe" too by
deriving it from .IRanges and not IRanges (see below).
- Reorganized the hierarchy of the BString class and subclasses by adding
the XString virtual class: now the BString, DNAString, RNAString and
AAString classes are all direct XString subtypes with no additional slots.
Most importantly, they are all at the same level in the new hierarchy
i.e. DNAString, RNAString and AAString objects are NOT BString objects
anymore.
- Reorganized the BStringSet and BStringList families of classes in a
similar way by adding the XStringSet and XStringList virtual classes.
Also now the XStringSet class derives from the .IRanges class instead of
the IRanges class so it is "safe".
- Added the XString() and XStringSet() versatile constructors. The BString()
and BStringSet() constructors and families are now based on them.
- Renamed subBString() -> subXString() and deprecated subBString().
No version bump yet.
rbsurv
for revision
xcms
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
prism
Removed usage (or reference) to pstricks tex style in BioC vignettes.
SLGI
change description file; removed suggests: YEAST
xcms
Fixed isCentroided if the center spectrum has only one peak
preprocessCore
(1.7.4) Fix bug with floating point argument provided where integer expected. Use of non intialized value.
[/preprocessCore] permanent link
affxparser
Bugfix in .initializeCdf thanks to bug report from E. Purdum
ctc
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
CoCiteStats
tried to rework some of this to make better use of the AnnotationDbi
interface
ctc
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affxparser
Fixed up writeTpmap as per bug report on BioC
Biostrings
Removed hard-coding of quality information in alignment related function.
Changed usage of deprecated function intToAdjacentRanges with successiveIRanges.
Added a QualityScaledXStringSet that can be weaved through Biostrings and ShortRead packages.
limmaGUI
Added NAMESPACE file
preprocessCore
(1.19.1 affyPLM) (1.5.1 preprocessCore) Fitting the default model using fitPLM() or rcModelPLM() now returns both probe effect estimate and corresponding standard error for the last probe in the model (note that the default model constrains the sum of the probe effects to be equal to 0)
[/preprocessCore] permanent link
Biostrings
[comments for previous commit + this commit]
- Added the trim() function for trimming the "out of limits" views of a
BStringViews object.
- Now the BStringSet() constructor (and family):
(1) fully supports BStringViews input,
(2) has a 'use.names' argument.
- Support the 'use.names' argument in the "unlist" method for ViewsIndex
objects.
maSigPro
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
ontoTools
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
xcms
Added score_fun man page
Added man page for simSearch.
changed plot.metlin so that x axes is the same on both plots
xcms
docu typo
S/N definition modified
allow adjacent peaks
Fix BinLinBase which had an uninitialised argument in .Call()
Biostrings
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Fixed a typo in man file.
Fixed the definition of XStringAlign class.
Set default for readFASTA() 'strip.desc' arg to TRUE (with a warning if the arg is missing).
xcms
Fixed plotSurf and image
ontoTools
dropped some setGenerics that were in conflict
for CHECK
simple changes to pass check
RpsiXML
small fix: unmatched right brace deleted
version bumping to 1.1.12, skipping 1.1.11 since this version has a large leap in the hypergraph object for complex data.
newly exported functions and methods, mainly for hypergraph objects
add/edit documents for newly strengthened hypergraph objects
add supporting methods mainly for psimi25Hypergraph, to make hypergraph objects more useful
add buildPCHypergraph, to build hypergraphs from protein complex file(s)
add hyperedgeNodes and edgeLabel, two generic methods mainly for hyperedges
annotate
Changed useHomology vignette so it won't interfere with build. Will replace with a new version soon.
GeneSelector
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/GeneSelector] permanent link
RpsiXML
Updated DESCRIPTION file to import XML, and added Collate field.
Rrsat
Removed usage (or reference) to pstricks tex style in BioC vignettes.
affxparser
Fixed a bug in readChp reported on Bioc mailing list, also fixed a problem in compareCels from yesterdays update of readCelHeader. This time it passes check.
VanillaICE
Changed biocViews entry of Statistics to Bioinformatics.
xcms
Fixed a serious fillPeaks() bug introduced in version 1.9.5, which caused it to
silently fill in zero intensities for almost every missing peak
Added check in findPeaks.matchedFilter() for not picking filter artefacts
Changed default mzdiff parameter in findPeaks.centWave() from -0.02 to -0.001
sizepower
Changed biocViews entry of Statistics to Bioinformatics.
BCRANK
Fixed uninitialized variable in C code
Biostrings
sync up with trunk
Small tweak to vmatchPattern()/vcountPattern(). Added support for indels to vcountPattern() (vmatchPattern() will follow as soon as MIndex objects support variable-width matches).
small tweak to findPalindromes()/findComplementedPalindromes()
Added support for indels to matchPattern()/countPattern(). Bumped version to 2.11.3
Refactored (and simplified) the C facilities for match reporting. Now they are entirely based on the AEbuf stuff from the IRanges package (this was a long due change).
xcms
OBSOLETED xcmsRaw@msnPeakNum and documentation fixes
VanillaICE
removed quotes from do.call
GLAD
modification pour compilation sous Windows et MAC OS
xcms
Various documentation/code fixups.
BGmix
Now uses Rmath.h, no need for GSL libraries
small change to Vignette
xcms
nomsg
Fixed unstated dependencies warning (Rmpi)
annotate
Version bump.
RpsiXML
Added hyperGraphSpeciesConverter
For converting incidence matrices and Hypergraphs.
Hypergraphs are only party supported untill someone adds the ability
to hypergraph to convert back from an incidence matrix to a
Hypergraph. For now, you can feed this function a Hypergraph, but it
will give you an incidence matrix in return.
This adds the function graphSpeciesConverter to RpsiXML
This new function allows a graphNEL object to be remapped to another
species. Neat!
siggenes
Small update of vignette caused by a change in rowttests.
rbsurv
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
biocGraph
biocGraph.Rnw now lists as its author the authors and maintainer of the
package, rather than myself.
ppiStats
edits to estimateCCMErrorRates.R
I have added man pages and updated the dependencies and namespace to avoid cyclic dependencies
flowClust
fixed Rd 2 parser warnings
xcms
Fixed leftover reference to faahko
updated NEWS file
GGBase
improve screen for bad anno
Biostrings
- The XStringSet and MIndex classes now contain the ListLike class (no-slot,
virtual) so they inherit the ListLike API ("lapply", "sapply" and "as.list"
methods are currently defined for ListLike objects).
- "neditStartingAt" and "isMatchingStartingAt" methods for XStringSet subjects
now return an m x n matrix (instead of n x m) where m is length(starting.at)
and n is length(subject). Same change for "neditEndingAt" and
"isMatchingEndingAt".
- Version bumped to 2.11.33
Biostrings
Added nucleotideFrequencyAt() (see ?nucleotideFrequencyAt). Bumped version to 2.11.56
limmaGUI
Added NAMESPACE file
xcms
added documentation about MS2spec and specinfo
ppiStats
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
sizepower
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Rdbi
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
nem
New functions and bugfixes.
graph
fixed bug in coercion method
ontoTools
fixup to pass check --- new litObj, more conditioning in vignette
Biostrings
Changes:
1) Swapped usage of RangesCollection with RangesList to follow changes in IRanges.
2) Added an as.matrix method for PairwiseAlignment objects.
3) Modified the consmat method for PairwiseAlignment objects to use the as.matrix results.
Minor change to man page example.
Added fasta.info() for fast extraction of the descriptions and lengths of the sequences stored in a FASTA file. Also renamed the 'strip.desc' argument of readFASTA() -> 'strip.descs'. Bumped version to 2.9.77
Added an as.matrix method for XStringSet-base classes.
flowClust
update README instructions for Windows users; move README to inst directory
SLGI
fix getSharedDomains which used to depend on environment based genome annotation package
affxparser
Fixed up writeTpmap as per bug report on BioC
miRNApath
Adds miRNApath to the 2.3 repos and manifest.
GGBase
ok
final pass
siggenes
Updated vignette.
affxparser
Version: 1.11.5 [2008-02-29]
o Updated cdfMergeStrands() to merge any even number of groups,
not only units with two or four group pairs.
o BUG FIX: The code in findFiles() for testing if R.utils is loaded
or not in v1.11.4 was not correct making it fail to detect R.utils.
Version: 1.11.4 [2008-02-20]
o Now findFiles() and hence findCdf() is only utilizing the R.utils
package if it is already loaded. It will no longer try to load R.utils.
o Added argument 'allFiles=TRUE' to findFiles().
o Updated readCcg() according to the newer file format specifications.
Now it is possible to do low-level reading of copy-number CNCHP
files generated by the Affymetrix Genotype Console v2.
maSigPro
make the man page more readable
BCRANK
Chenged the progress status output
preprocessCore
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/preprocessCore] permanent link
Biostrings
Two small changes in alphabetFrequency():
(1) when used with 'baseOnly=TRUE', the frequency of the gap letter ("-") is
not returned anymore (now it's treated as any 'other' letter i.e. any
non-base letter);
(2) added the 'freq' argument.
Added the dinucleotideFrequency(), trinucleotideFrequency(),
allOligonucleotideFrequency() and mkAllStrings() functions.
Renamed some files in inst/extdata/ to use the same extension (.fa) for all
FASTA files.
Version bump.
HEM
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
HEM
Removed usage (or reference) to pstricks tex style in BioC vignettes.
Biostrings
update TODO
Biostrings
Renamed 'data' slot (XString class) -> 'xdata'. Version bumped to 2.7.43
limmaGUI
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
siggenes
Removed support for soon to be defunct class exprSet.
xcms
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Added missing dev.off(), fixing MacOS now ?
RpsiXML
I am populating the new package RpsiXML
Biostrings
Added a mismatchSummary function.
Fixed rep methods for zero-length AlignmentXStringSet and PairwiseAlignment objects.
Fixed handling of 'weight' argument in "coverage" method for MaskCollection objects.
Fixed problem with the "rep" method for IRanges objects when 'x' is of length 0.
Some minor improvements to IRanges_coverage() C function.
Version bumped to 2.9.36
Added a summary method for PairwiseAlignment objects.
xcms
Revised pipeline framework. Documentation forthcoming. Comments greatly
appreciated.
dyebias
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
BCRANK
New default values, small change in manual
PAnnBuilder
Cleaned up vignette to use biocLite and only mention *.db packages.
Removing eval from library installation in vignette.
Corrected small mistake in the vignette about installation.
Since this package is now part of Bioconductor, the correct
installation is to use biocLite(), Doing so will correct a problem
that was happening on the MAC and also ensure consistent knowledge of
which version of things users are getting in the future.
Biostrings
Renamed the BStringViews class -> XStringViews (long due change!). Bumped version to 2.7.52.
Implemented the quality-based substitution matrix method of Ketil Malde.
dyebias
Bumped version to 1.3.1 (tought I already done that)
using median of ratios rather than ratio of medians, and concommitant changes. See ChangeLog
Biostrings
Added a new qualitySubstitutionMatrices function for quality adjusted alignments.
Bumping the version number so recent changes will be included in next build.
Adding a new compareStrings function for looking at aligned strings.
Added an inserts accessor method for AlignedXString class.
Fixed a bug in the profile calculation in pairwiseAlignment.
Made alignScore function defunct.
Fixed two bugs in pairwiseAlignment, one in the traceback procedure and one when there is no alignment.
Biostrings
Added a section on Removing Adapters from Sequence Reads to the alignment vignette.
annotate
wrapped the p2LL example in dontrun as the function is now deprecated
RpsiXML
HPRD support compatibility is improved by recognizing PubMed reference
version bumping: improved compatability with MPact data
.parsePsimi25Experiment improves compatibility with MPact: PUBMED is taken as pubmed
export MPACT.PSIMI25, version bumped
Biostrings
Removing integer specification from substitution matrix.
Allow users to specify XString objects for the string quality scores in pairwiseAlignment.
Modified how character based quality scores are converting into [0, 1] metrics during pairwiseAlignment.
Added the ability to use characters for the quality measures of the strings in pairwiseAlignment.
To the pairwiseAlignment function:
1) Added a scoreOnly parameter for returning just the score (and not that alignment).
2) Renamed matchScoring parameter to substitutionMatrix.
Biostrings
Changed the term constant substitution matrix to fixed substitution matrix.
Biostrings
Added 'append' arg to writeFASTA(), write.XStringSet() and write.XStringViews() functions.
flowClust
Adds the flowClust package to bioconductor.
Biostrings
Switched to R's definition of negative infinity to avoid worry of overflow in order to speed up calculations in pairwiseAlignment.
Biostrings
Added neditStartingAt(), neditEndingAt(), neditAt(), isMatchingStartingAt(),
isMatchingEndingAt() and isMatchingAt(): they all support indels via the
'with.indels' argument. Deprecated nmismatchStartingAt(), nmismatchEndingAt()
and isMatching().
Biostrings
Small improvement to save.XStringSet(). Bumped version to 2.13.34
nem
Bib File added.
xcms
Migrate to ncdf for xcmsRaw.write()
changed part about xcmsRaw return value. via Colin
hypergraph
Fixed a matrix subscripting bug and an unlist related warning.
be more careful with parameter names
ppiStats
edits to ppiStats.Rnw
adding vignette ppiStats.Rnw
xcms
Add missing docs.
syslibGTK
changed order in PKG_CONFIG_PATH for Mac
keggorth
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
xcms
Adding back the package cleaning to Makevars.
RpsiXML
Trivial change: Description file the contact info of Tony completed; validate file function temporarily not exported so the test lines are also commented out
validate function does not export for now
Biostrings
Added a degap argument to AlignedXStringSet method of aligned function.
Removed unneeded quality measures from aligned() function calls for quality-based alignments.
Fixed narrow and append bugs for QualityScaledXStringSet objects.
Minor speed up to set operations for XStringSet objects by finding the uniques prior to conversion to character.
Fixed bug in creating zero length PhredQuality and SolexaQuality objects.
VanillaICE
fixed bug in calculation of emission probability...
xcms
fix for pipeline()
affxparser
Added a Makefile, bumped version
Fixed small as.integer() bug in tpmap2bpmap
Biostrings
Trying to have inst/include/_Biostrings_stubs.c understood by Sun Studio 12 C compiler. Bumped version to 2.11.47
Fixed 2 issues with new "consensusString" method for matrices (division by 0 + bad output format).
siggenes
Moved buildSNPannotation and shortenGeneDescription to the package scrime which is now suggested by siggenes (future changes in siggenes for the analysis of SNP data will essentially make use of the functions in scrimes).
pcaMethods
fixed Rdversion 2 parser warnings
graph
adding defaults to the nodeRenderInfo data
graph
fix .ftM2other() for "self-edges"
VanillaICE
added hmm.Rd
siggenes
New license: siggenes is now available under LGPL.
Preparation for major update in which several methods for SAM and EBAM will be added: Renaming of arguments data and cl (to x and y).
Removed file/folder
Added a file remotely
Removed file/folder
Biostrings
Added a check to ensure string qualities are of the same class during the alignment process.
Fixed issues in reverseComplement related to moving some reverse functionality to IRanges package.
Added new XStringQuality classes to make it easier to manage string quality information.
Biostrings
[code cleaning] Use of macros in C code in charge of .Call entry points and C callable registration. This makes the code cleaner, shorter, and easier to read/maintain.
Removed Auto-Extending buffer local implementation. C code that deals with AE buffers is now calling the AE functions that are part of the IRanges C interface. Bumped version to 2.9.57
Biostrings
More cleaning of the ByPos_MIndex/ByName_MIndex mess.
The ByName_MIndex class is not exported, not documented anynmore. The
ByPos_MIndex class (and any MIndex subclass in the future) now can hold
names. Removed 'all.names' arg from "startIndex", "endIndex" and
"countIndex" generics and methods. Made unlist() and extractAllMatches()
work on any kind of MIndex object. vmatchPattern() now propagates the
names of the subject. Bumped version to 2.11.40
RpsiXML
getNamedElement is modified similar as elNamed to save parsing time
Release 1.5.20: scaffold list objects are removed to accelerate the parsing. The parse time reduces by ca. 25%. See the NEWS file along the release
Biostrings
Bumping the IRanges version dependency.
Removed generics for chartr, substr, and substring to avoid conflicts with other packages (e.g. IRanges) that also define methods for these base functions.
xcms
removed quotes from do.call
flowClust
bumping flowClust version to 2.0.4
minor updates to documentation files
a fix to Map.Rd
Biostrings
Fixed the weights argument in summary method for PairwiseAlignment arguments.
Fixed a bug in subsetting method for QualityAlignedXStringSet objects.
Expanded the range of qualityType for "Solexa" to [-5, 99].
Minor speed up enhancements to pairwiseAlignment function.
Minor speedup enhancements to alignment utility functions.
xcms
Removed obsolete xcmsProtoGenProfileBase
centWave : fixed two small bugs related to gauss fits
added warning if identical scantimes exist, can indicate converter problems.
Added hra_clust for m/z alignment to xcmsSet
Added getMsnScan to xcmsRaw for Tandem MS / Ion Trap data
RpsiXML
fix the Imports field in DESCRIPTION
fix Rd issues found by Rdversion 2 parser
RpsiXML
complex accesors wrapped into methods, bait/prey accession added
accession/baitAccession/preyAccession methods added to extract accession numbers of the database (different from sourceId, where the id might be a auto_increment integer index within one XML; complex accessors wrapped into methods
xref turned into generic method
xrefDb and xrefId unlist first
version bumping: accessors uniformly wrapped in methods
accessors uniformly wrapped into methods
accessors uniformly wrapped in methods
interactionEntry2graph method refactor: hide slots with functions, bait/prey instead of @baitUniProt and @preyUniProt
VanillaICE
several updates to make the package compatible with SNPchip. Changed the annotation field in chromosome1 as well as the fvarLabels. Updated the vignette
xcms
Finished manpage
Adapted Warning message to parameter name change
BGmix
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GGBase
ok
xcms
Call phenoDataFromPaths(files) only if necessary
Call phenoDataFromPaths(files) only if necessary
VanillaICE
changed the function calculateCnSE allows missing values for copy number. changed the show method for HmmPredict class
GGBase
various
Biostrings
Minor refactor to mismatchTable to speed execution.
Adding quality measures to mismatchTable output.
Modified the narrow man page to reflect recent changes.
1) Enhanced the narrow function to accept vectorized start/end/width arguments.
2) Renamed the mismatch method for PairwiseAlignment objects mismatchTable and added the ability to widen the view around the mismatch to see neighboring letters.
Biostrings
Added an is.unsorted method for XStringSet objects and removed XStringSet_in_set since the cost of its maintenance outweighed the speedup it had over using match to produce %in% output.
Make NCBI download of BLOSUM matrix condition on being interactive to avoid unimportant R CMD check errors.
Small adjustments to the recent changes/additions:
- MIndex now contains IRangesList (more accurate than RangesList).
- Removed XStringSet_not_duplicated C code (not needed, having
the XStringSet_duplicated C code is enough). The same would
probably apply to the XStringSet_in_set/XStringSet_match C code
(seems redundant).
- Fixed segfault in "rank" method for XStringSet objects when
the object has no elements.
Added doc for fastq.geometry().
Fixed a bug in duplicated method for XStringSet objects when length = 1.
SMAP
Changed biocViews DNACopyNumber to CopyNumberVariants and SNPsAndGeneticVariability to SNP, GeneticVariability.
Biostrings
Added the compact() generic. Bumped version to 2.13.5
BCRANK
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowClust
modified .ellipse() to get rid of the precision problem arisen due to the large difference in the lengths of the two axes of an ellipse
xcms
Added FTICR calibration
VanillaICE
fixed bug in calculateBreakpoints. Removed ParHmm* classes
CoCiteStats
this is going to break until the paperLen issue is resolved, but at least
humanLLMappings is gone, for now
this is going to break
Biostrings
time to bump the version (to 2.9.14)
Fixed a bug in pairwiseAlignment when type = patterOverlap or subjectOverlap.
Created a consmat method for PairwiseAlignment objects.
Minor help file edit.
Moving scoring in pairwise alignment to the bit scale.
GGBase
it installs
GGBase
introduce the sqlite backend for snplocs ... netcdf not adequate
dropping netCDF
new vignette
dropping the netCDF approach, using SQLite for snp locations
xcms
findPeaks.centWave: generates a warning if data seems to be not in centroid mode
findPeaks.centWave: generates a warning if data seems to be not in centroid mode
findPeaks.centWave: generates a warning if data seems to be not in centroid mode
Biostrings
Added PairwiseAlignment constructors so users can input their own prefit alignments.
Added a toLatex statement to sessionInfo.
xcms
findPeaks.centWave:?\194?\160narrow?\194?\160down?\194?\160peak?\194?\160rt?\194?\160boundaries?\194?\160by?\194?\160skipping?\194?\160zero values
HilbertCurveDisplay
added GFF parsing
added code for stand-alone version
[/HilbertCurveDisplay] permanent link
ppiStats
I have updated the function to estimate fpfn rates for ppi data
limmaGUI
Added GUI biocView to DESCRIPTION file.
GLAD
correction des WARNINGS
modification de la d?\195?\169pendance au package tcltk
ppiStats
i have updated both the code to find the error rates
gaggle
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xcms
Import xcms from BioC 2.1
Final commit as 1.11.18
RpsiXML
on 12.12.08 the package failed by checking, the reason for that is (1) depends in 'DESCRIPTION' miss XML and hypergraph (2) import in 'NAMESPACE' doesn't need hypergraph. Fixed version passes the R-devel check without error
a latent debug in file testing when corumxml exists is fixed
xcms
findPeaks.centWave: m/z ROI search: debug option was still enabled
RpsiXML
ChangeLog (produced with svn2cl) added
Syntax fix: windows will warns the user not supported
Syntax fix: non-generic functions have been removed from genericFuns; validatePSIMI25 is now exported
Bug fix in psimi25XML2Graph: if bait and pray list contains NA, they will be replaced with character NA in order to avoid the cases where the genBPGraph method has to select a NA row/column from a matrix. I still wonder how we can treat the identifier better, can we get a function to build a graph based on source code and then convert them to uniprot? It is not easy to translate uniprot to other identifiers: imagine a sourceID without Uniprot but with other annotation, say MIM, you then have a NA as the uniprot, which means you have actually lost your source ID and its information.
nem
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
ppiStats
updated the depends files
affxparser
Version: 1.15.4 [2009-02-10]
o readCcg() and readCcgHeader() no longer give warnings
on 'truncating string with embedded nul' in rawToChar().
These warnings made no difference, but were annoying.
Version: 1.15.3 [2009-01-22]
o Fixed a minor Rd problem.
Biostrings
Added a Quality Assurance in Sequencing Experiments section to the Alignments vignette.
Added an errorSubstitutionMatrices function for instructional purposes.
Added a section illustrating the usage of BLOSUM and PAM matrices in pairwise sequence alignments.
Added a section on Removing Adapters from Sequence Reads to the alignment vignette.
xcms
findPeaks.centWave: Optimizations for OrbitTrap/FTICR data, different methods can be used for calculating the m/z center of the feature: mzCenter.{mean,wMean,apex,wMeanApex3,meanApex3}
Fixed: maximum intensity (maxo) was incorrect for some features
VanillaICE
fixed bugs in copynumberEmission
timecourse
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
Major refactor to the IRanges package. The class system became unwieldy and we decided to make the Sequence virtual class the parent of nearly all classes in this package, much like the vector virtual class is the parent of nearly all classes in the S3 world.
affxparser
Fixed the loading of R.utils in findFiles. This loading had bad consequences for R CMD check - unfortunately. A better fix would be to take care of the problem at its root.
Biostrings
Fixed small problem in "initialize" methods for Twobit and ACtree objects.
Resync with latest changes in IRanges (1.1.7). Bumped version to 2.11.14
Fixing a bug in pairwiseAlignment when scoreOnly = TRUE and using Rmpi.
nem
New functions: Plotfunction, nearest transitive approximation. Bugfixes.
xcms
fixed some documentation prolems
GGBase
add snpsNear
DynDoc
fixed the documental mismatches warnnings pertained to
vignetteCode-class.Rd.
Fixed check warnings for document mismatches existed in
getPkgVigList.Rd, vignetteCode-class.Rd and chunkList-class.Rd.
Bumped up version number o 1.23.1.
RpsiXML
Rintact is unloaded after using ppiStats to avoid conflict of methods
Update version: add Application Example Vignette
RpsiXML.Rnw preamble slightly change; add RpsiXMLApp.Rnw for application examples of RpsiXML package
keggorth
Removed usage (or reference) to pstricks tex style in BioC vignettes.
graph
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
annotate
some extras
annotate
Minor adjustments.
nem
Several new functions. Bugfixes. Merged files.
DEDS
Changed biocViews entry of Statistics to Bioinformatics.
GGBase
ok
improve validation
Biostrings
Added a weight argument to the coverage function to allow for different weight counts for the elements of an IRanges object.
Minor code change for minor performance improvement to pairwiseAlignment.
GGBase
trying to fix up the docs so we don't get warnings on windows
flowClust
Using pkg-config in configuration to make it easier to build against the GSL library.
HilbertCurveDisplay
added function "makeWiggleVector"
[/HilbertCurveDisplay] permanent link
graph
updateGraph now issues a warning message when applied to up to date objects
fixed a bug in edgeRenderInfo<- caused by NULL assigments
Biostrings
Rename internal C function compute_score to compute_pwm_score to avoid confusion with future score computing functions.
Cleaned up comments in matchPWM method for XStringViews objects.
Biostrings
Added an example showing an alternative algorithm for mapping probe set IDs between chips (has even more restrictions than the first algorithm).
Improved vwhichPDict() speed by using vmembers() internally for
adding the ids of the duplicated patterns to the result.
Added a full example showing how to use it to map probe set IDs
between chips.
Bumped version to 2.13.2.
maSigPro
Fixed imports and exports in NAMESPACE file.
GGBase
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
DynDoc
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowClust
fixed access to parameters slot which has changed in flowCore
RpsiXML
version up to 1.1.20
hypergraph imported
inciMat2HG is supposed to be inciMat in 'hypergraph' package, fixed
update to 1.1.19: enable multiple baits
getDesired function fixed to enable more than one baits in one interaction. Baits and preys without UniprotKB annotation will be omitted in 'separateXMLDataByExpt' function.
Biostrings
Further simplification of TypedList class to make it easier to maintain.
SLGI
fix iSummary to handle deprecated GO terms
RpsiXML
Bumping the verison number for release prep.
annotate
Swapped usage of old style deprecated annotation paradigm with new AnnotationDbi paradigm.
Biostrings
Change pairwiseAlignment to support insertions followed immediately by deletions and vice-versa.
Added a new oligonucleotideTransitions function to make it easy to generate transition matrices.
Removed subjectViews function and make views a generic S4 function that combines views with subjectViews. Also, made minor bug fixes to better handle bad inputs to various functions.
ontoTools
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
DEDS
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
preprocessCore
(1.5.3) fix VECTOR_ELT/STRING_ELT issues
[/preprocessCore] permanent link
affxparser
Moved readPgf, readClf to *Env, added readPgf,readClf,readClfHeader,readPgfHeader. These now return lists and use an indices argument to specify which probesets should be read. The value of these over the environment function is questionable.
updated to Fusion 1.0.10b
biocGraph
added XML to the suggests
Biostrings
Moved (and adapted) the matchprobes vignette to Biostrings. Bumped Biostrings and matchprobes versions to 2.11.30 and 1.15.5, respectively.
Biostrings
Added content to the Computation Profiling section of the Alignments vignette.
Added a bibliography to the Alignment vignette.
Added a Quality Assurance in Sequencing Experiments section to the Alignments vignette.
VanillaICE
Changed biocViews DNACopyNumber to CopyNumberVariants and SNPsAndGeneticVariability to SNP, GeneticVariability.
xcms
Fixed xcmsPipeline for character literal arguments
Fixed a bug in findPeaks.centWave: NaN was assigned as peak intensity in some rare cases
added manpage for findPeaks.MS1
xcms
Fixes in Obiwarp alignment
maSigPro
maSigPro NAMESPACE
Heatmap from EMV package removed.
graph
fixed a bug in the setter for edgeRenderInfo
some clarification of the documentation for renderInfo. More might be needed later
xcms
more robust MSn reading
more robust fillPeaks.mean
Remove documentation of removed argument
Fixed groupval() call in Vignette
VanillaICE
added accessors/replacement methods for HmmOptions class
BCRANK
Removed strip.desc argument to readFASTA. Not supported in Biostrings < 2.8
DynDoc
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
Change TypedList class to inherit from ListLike class.
Biostrings
Added predefined RNA_GENETIC_CODE object and completed man pages for IUPAC_CODE_MAP and GENETIC_CODE.
Modified example for matchPWM() so it works with new version of BSgenome.Dmelanogaster.UCSC.dm3 (starting with BioC 2.3, BSgenome data packages will contain masks that are active by default). Bumped version to 2.9.60
RpsiXML
Version 0.0.7: MPact is supported now.
annotate
Removed assumption in calling mget() and also corrected codoc mistmatch.
maSigPro
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
xcms
Adding Steffen as a package author
Fixing a couple coding/documentation bugs in plotTIC
graph
minor problem in pancrCaIni.Rd
MAPKsig graph data is misleading; pancrCaIni pathway graph example to supersede
xcms
Fixed Bug in group() with unused class levels
gaggle
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
siggenes
Fixed a few bugs in make.tablecode (utility function of sam2html and ebam2html).
CoCiteStats
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affxparser
Added a check to make sure that the indices are sorted for now. The larger fix requires reading the file in a different way because of the linked list type setup. Or it requires a little bit of fixing up on the way out, which might be the appropriate way.
VanillaICE
changed Description
GLAD
version 2.2.3
ajout de fonction C/C++
annotate
Bug fix for PWAmat()
This just makes the PWAmat() a little smarter so that it will not
explode when it runs into an NA.
CoCiteStats
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
MIndex objects: added width0() + C-level caching facilities and abstract accessors. Bumped version to 2.13.28
annotate
Version bump for the fix in previous checkin.
preprocessCore
(1.1.8) Commit missing header files
[/preprocessCore] permanent link
Biostrings
Another change to the CWdna_PDict class (the @dups slot is back, the SparseList are gone, @dups is now of type Dups and is twice bigger than the old @dups) in order to fix PDict() performance issue when the input dictionary contains highly repetitive reads. Version bumped to 2.9.18
Changed the definition of compareStrings.
SLGI
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Biostrings
First working version of the preprocessing and fast matching of the head and tail of a PDict object. Still needs some testing.
hypergraph
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
rbsurv
Updated eSet object and bumped version number.
xcms
minor code beautifications
annotate
Replaces a couple of lost Entrez Gene www functions.
This just replaces a couple of functions that had been removed due to
many changes in the annotation packages (locusLinkByID() and
locusLinkQuery()) with new functions entrezGeneByID() and
entrezGeneQuery() which are as true to the original spirit of these
functions as I could make them (they each make URLs that will take you
to the relevant data at NCBI).
Biostrings
Added support for a constant mismatch rate when trimming.
Added more explicit documentation of max.Lmismatch and max.Rmismatch and pad -1's to these vectors when they are too short.
Modified the meanings of max.Lmismatch and max.Rmismatch arguments to better match typical use cases.
syslibGTK
Adding a syslibGTK package for Simon Anders.
xcms
Added polarity to xcmsRaw and import of mzData / mzXML
Biostrings
Added "maskedwidth" and "maskedratio" methods for MaskedXString objects. Filled some gaps in man page for these objects.
miRNApath
Fixed bug in runEnrichment with pathway permutation P-values, specifically with permutations showing enrichment in only a subset of overall pathways.
keggorth
updated serialized graph object
sizepower
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
GLAD
version 2.2.6
BCRANK
Crucial bug fix for R 2.8 (again)
Crucial bug fix for R 2.8
flowClust
fixed access to parameters slot which has changed in flowCore
some changes to cope with recent redefinition of "parameterFilter" class in flowCore (the "parameters" slot now takes a "parameters" object (which is a list) instead of a character vector; changed tmixFilter function and %in% method accordingly)
Biostrings
Added more functionality to support position weight matrix activities.
gaggle
get version number programmatically
fixed typos
VanillaICE
updated illuminahowto vignette
affxparser
Version: 1.15.2 [2008-12-30]
o Same bug fix as in release version v1.14.2.
Version: 1.14.2 [2008-12-30]
o BUG FIX: readChp() would not read all data. Thanks
Gabor Csardi for reporting this and providing a patch.
xcms
Fixed plotScan() for last spectrum, catch out-of-bounds arguments
Increased "max" parameter of group() from 5 to 50
biocGraph
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affxparser
Fixes include statements in Fusion, trying to fix an issue with GCC 4.3. Fix suggested by Herve Pages
VanillaICE
allow option to plot vertical dashed lines for breakpoints. Updated the fit example data
BCRANK
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
VanillaICE
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
ppiStats
add findAdjacent to NAMESPACE
added findAdjacent.R and .Rd
Biostrings
oligonucleotideFrequency(): some code optimizations.
oligonucleotideFrequency(): the "shape" of the answer is now controlled
thru the 'as.array' and 'simplify.as' arguments.
oligonucleotideFrequency():
- Replaced 'as.array' arg by 'as' arg.
- Return a matrix by default on an XStringSet object.
- Moved top-level loop in method for XStringSet objects to the C level
(except when 'as' is not "atomic" and 'collapse' is FALSE).
Biostrings
moved the RawPtr class to the IRanges package so that the RawPtr/IntegerPtr/NumericPtr family is together again
dyebias
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
affxparser
fixed a minor doc bug
GGBase
some new classes
Biostrings
Resync with latest changes in the Partitioning class in the IRanges
package. Bumped version to 2.13.3
pcaMethods
mistake..
Fixed slplot so that it accepts differnt arguments for the scores and loading plots and complains if sl and ll are of wrong size. Added a show method as that often is the default function and not print. Small bugfix in nipals pca. Nipals pca is however poorly tested and might change again soon.
siggenes
Removed usage (or reference) to pstricks tex style in BioC vignettes.
Biostrings
The first draft of a matching method based upon weighted clustered positions (WCP), a conceptual generalization of matching based on position weight matrices. This new scheme uses three new categories of classes: XKeySortedData, XKeySortedDataList, and WCP. This check in also made some improvements to maxScore/maxWeights (PWM) and XStringSet infrastructure.
Fixed a bug in pairwiseAlignment when scoreOnly = TRUE and gapOpening = 0.
limmaGUI
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
Added the "palindromeArmLength", "palindromeLeftArm" and "palindromeRightArm" generics and methods. Added a man page for all the palindrome related functions.
siggenes
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
pcaMethods
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
Biostrings
Reworked the findPalindromes() API:
- change in terminology to align with established practices: "antipalindromes"
are now called "complemented palindromes" and "the gap" between the 2 arms
is now called "the loop";
- no more 'anti' arg: use findComplementedPalindromes() to find complemented
palindromes;
- the 'max.ngaps' arg has been renamed 'max.looplength';
- there is a new 'min.looplength' arg (not yet supported);
- there is a new 'max.mismatch' arg (not yet supported);
See ?findPalindromes for more details.
Applied "matchPDict() boost feature" patch
With this patch, finding all the matches of a 3.3M 32-mers dictionary in the
full Human genome (+ and - strands of all chromosomes) is about 2.5x faster
than before (will take between 20 minutes and 2 hours depending on the machine
and the number of matches found). This puts matchPDict() at the same level as
the Vmatch software (http://www.vmatch.de/) for a dictionary of this size.
Memory footprint for matchPDict() is still reasonable: between 500M and 800M
for the Aho-Corasick tree built from the 3.3M 32-mers dictionary. Building
this tree is still very fast (2 or 3 minutes) (Vmatch needs 60G of disk space
to build all its suffix arrays, don't know how long it takes for this, don't
know what's the memory footprint either when they are loaded into memory but
it looks like it is several Gigas).
There is still room for making matchPDict() even faster (10%, maybe 20%).
Reminder: matchPDict() still only works with a dictionary of DNA patterns
where all the patterns have the same number of nucleotides (Vmatch doesn't
have this kind of limitations). This can be addressed in the future depending
on the kind of applications we want to target (our main goal for now is to be
able to work with Solexa data).
Version bump.
affxparser
Really updated to Fusion 1.10b. Fixed an error in the help page for readCel.R
ontoTools
various objects updated
maSigPro
Replaced a call to the deprecated read.exprSet function with readExpressionSet.
xcms
Started fixing manpage to match Code
maSigPro
Added a namespace to the package and updated description file
xcms
Fix xcmsRaw() for non-XML input
New findPeaksMS1() to report precursor peaks
xcms
Rework file name computation in xcmsSet(). Fix missing symbol in
profileMatrix<-().
Cleanup mzClust code
affylmGUI
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
keggorth
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
ontoTools
ok
timecourse
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
rbsurv
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
ppiStats
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
Fixed the traceback when insertions are immediately followed by a deletion and vice versa in pairwiseAlignment.
Change pairwiseAlignment to support insertions followed immediately by deletions and vice-versa.
VanillaICE
calls.ICE should be working now. updated vignettes
BGmix
unsupported on Windows
GGBase
sdf
VanillaICE
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
VanillaICE
the viterbi algorithm was not handling NA emission probabilities appropriately. should be OK now
annotate
more bug fixing and version number bump
dropped some functions that have not worked for more than a year (no
deprecation/defunct cycle needed since they cannot have been used)
xcms
Fix NAMESPACE for new stages.
Add prompt methods for stages and protocols. Remove filterProfile stage
(and filterProfileBase protocol) and replace with more specific (and
thus hopefully clearer in purpose) stages removeProfileBaseline and
smoothProfile. Various other fixes.
Agi4x44PreProcess
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/Agi4x44PreProcess] permanent link
Biostrings
Added 'append' arg to writeFASTA(), write.XStringSet() and write.XStringViews() functions.
Fixed a minor typo.
Added a conversion method to go from MIndex objects to CompressedIRangesList objects.
GGBase
snpsNear to SNP
serious bug in smlSet[ chrnum, ] repaired
Biostrings
Small inprovement to C-level Boyer Moore. Added match_pattern_boyermoore() to the C interface. Bumped version to 2.13.29
RpsiXML
Updated graph Converter functions to be more generically useful.
Newer functions in AnnotationDbi allow for these functions to be able
to be generically converted even if the source and destination species
are the same.
dyebias
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
Minor code changes for marginal improvements.
Added the ability to use pairwiseAlignment when the pattern object is an XStringSet argument when scoreOnly = TRUE. This involved a refactoring of the code and a renaming of some arguments.
xcms
Added reading of MSn spectra
GGBase
change show method for smlSet
Biostrings
Added more information of alignment functions and added a section on edit distances.
Changing the alphabet length for BString objects to 256 rather than the observed length in pairwiseAlignment.
1. Added a toString method for PairwiseAlignment objects.
2. Fixed a bug in mismatchTable & mismatchSummary to handle case when there are no mismatches.
3. Fixed a bug in pairwiseAlignment to handle case when there is only one character in a BString quality-based alignment.
preprocessCore
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/preprocessCore] permanent link
Biostrings
Fixed small regression (introduced at r33613) in [[ operator for MIndex objects. Bumped version to 2.11.5
Unit tests for PDict and matchPDict
- Fixed a few inaccuracies in man/matchPattern.Rd.
- Now man pages for matchPattern() and pairwiseAlignment() both make reference
to each other.
annotate
Changes to htmlpage(). The repository argument must now be a list. Deprecated the 'LL' functions in lieu of the 'EN' functions, intended for querying Entrez Gene. Also ceased exporting internal function used by htmlpage such as getCells(), the getQuery4XX functions, etc.
minor bug fixes for htmlpage, also seem to be issues with the way
that character data are being stuck into data.frames - they come out AsIs
and that breaks lots of things
BGmix
Bumped the version number to prepare for BioC 2.2 release.
preprocessCore
(1.3.1) rma.background.correct() was not correctly returning value when copy ==TRUE
[/preprocessCore] permanent link
RpsiXML
ADD TODO: I gonna implement the function in this week
RpsiXML
have updated the package so that it works with a newer version of one particular IntAct XML file and added example XML files for the useR book
Biostrings
Added subsetting operation to PairwiseAlignment objects.
Minor formatting edits.
Allow insertions immediately followed by deletions in score only calculations by pairwiseAlignment.
xcms
Resurrection of 1.11.18 in TRUNK
affylmGUI
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
ctc
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
syslibGTK
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
Biostrings
Adjusted hard-coded limit in order to support 'max.nedit' values up to 100. Bumped version to 2.13.16
Fixed a comment in XStringViews_match_PWM
Biostrings
Added the 'collpase' arg to alphabetFrequency() and family. Version bump.
ppiStats
Fixed YEAST to org.Sc.sgd problems.
limmaGUI
fixed Rdversion 2 parser warnings
Biostrings
Add the "ACtree2" container.
This container uses a more compact representation of the Aho-Corasick tree
that results from preprocessing a Trusted Band. It is an attempt to address
the problem of the size of the "ACtree" container currently in use in PDict
objects. With this new representation, a node can occupy either 8 bytes (2
ints) or 28 bytes (7 ints) in memory, depending on whether it's "extended"
(i.e. it has >= 2 links) or not (i.e. it has 0 or 1 link). Some testing with
less than 30% or 40% get extended during the typical life of the PDict object
(e.g. after it has been used on a full genome). This should reduce the size of
PDict objects by at least a factor of 2 with no major impact on performance
(no more than 10%, but it could be much less, this still needs to be verified).
This reduction in size plus some specificities of the internal representation
of ACtree2 objects allows preprocessing of Trusted Bands made of > 60 millions
35-mers (on machines with enough memory).
Biostrings
Got rid of load-time warnings:
Warning in namespaceImportFrom(self, asNamespace(ns)) :
replacing previous import: head
Warning in namespaceImportFrom(self, asNamespace(ns)) :
replacing previous import: tail
Bumped version to 2.11.51
"consensusMatrix" method for XStringSet objects: added some details
about the 'width=NULL' mode
Make use of the new coverage() interface. Bumped version to 2.11.50
xcms
Fix fixed getEIC
gaggle
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GGBase
change show method for smlSet
Biostrings
Expanded the print width for R io in Alignments vignette.
even more changes reflecting latest changes in the IRanges package
more changes reflecting latest changes in the IRanges package
GGBase
fixed Rd version 2 parser warnings
flowClust
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
xcms
Added low-level debugging in vignette to hunt down SEGV on MacOS 10.4
xcms
Fix SET_ELEMENT error with recent R-devel for character vectors
Fix warnings in manpages
Fixed typo in default argument
Much work on findPeaks.MSW and new fillPeaks.MSW
rbsurv
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
HilbertCurveDisplay
Fixed a few typos and inserted FIXMEs in the vignette.
[/HilbertCurveDisplay] permanent link
ontoTools
Fixed outdated KEGG dependency.
There is still a problem with the vignette that will have to be fixed
where the files in rdata are bumped in the vignette but not in the
data file.
ppiStats
I have updated the DESC to work with the NS file so it passes build and check
ppiStats
I have updated sumStatCharts by adding three new functions
GGBase
ok
put ... in plotter function for cwSnpScreen
fix doc for check
keggorth
Added a namespace to the package, Added biocViews terms
preprocessCore
(1.1.9) Commit missing c source files. This should allow preprocessCore to successfully build and also pass R CMD check (which it has not done since 1.1.6)
[/preprocessCore] permanent link
annotate
Revised import of AnnotationDbi to include only a subset of the package.
Replaced tab with spaces.
Bumped the version number.
graph
lots of code refactoring for the combineNodes function. We still need to decide how to treat edge weights of combined edges
Biostrings
Removed unneeded R code.
Enhanced the nedit* functionality.
Make coverage method for MIndex objects return Rle instances.
Biostrings
Fixed some bugs in trimLRPatterns and added support for ragged length subjects when using Rpattern.
HEM
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xcms
Add check against c()ombining xcmsSets with overlapping sample names
RpsiXML
Release 1.5.15: most of the entry elements have their handlers. See NEWS for details
Release 1.5.14, code name 'Amsterdam Afternoon'. Data structure changes not visible to end user yet. See the NEWS file released along the package for details
graph
combineNodes now takes an optional function to collapse the edges
Biostrings
Added a consmat method for AlignedXStringSet objects.
Minor edit to consmat message.
Changed the show method of PairwiseAlignment and AlignedXStringSet classes to handle case when length(object) == 0.
SLGI
add function (shareIntMat) to search for pleiotropic gene
xcms
findPeaks.centWave: changed minPtsAboveBaseLine to max(4,minPeakWidth-2)
Biostrings
Replaced usage of subXString with subseq in vignette.
RpsiXML
Release 1.5.18: confidenceType handler added; profiling in progress
Release 1.5.17:All PSI-MI 2.5 elements have handlers
Biostrings
Refactor to support usage of PairwiseAlignment name in IRanges. Changed PairwiseAlignment class to PairwiseAlignedFixedSubject and added a PairwiseAlignedXStringSet class.
Biostrings
Added a rank method for XStringSet objects.
Added handling of empty XStringSet in unique and duplicated functions.
Added a first pass at unique and duplicated methods for XStringSet objects.
Biostrings
Minor change to man page.
xcms
xcmsSet: added getScanWindow() and plotScanWindow() which provide
the same kind of graphics for direct-infusion spectra
as xcmsEIC does for LC-MS
siggenes
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Biostrings
Moved the coverage calculations for IRanges down to C to speed up calculations.
Merged the latest changes from the testing branch of Biostrings [merge -r 32268:32356]. This is a complete redesign of the PDict class hierarchy and the PDict() constructor (see NEWS file for the list of visible changes). Also fixed the problem with matchPDict()/countPDict() raising a silly error when the 'pdict' argument didn't contain all the DNA base letters.
Biostrings
Adding entry for PWMscore function in the usage block.
BCRANK
New function for reporting predicted binding sites
RpsiXML
version bumped to 1.1.4: updated support for CORUM: now it can parse uniprot
CORUM uniprot identifier changed from 'swissprot' to 'uniprot knowledge base'
psi25parser remains using simple pubmed
graph
Standardizing reference to Artistic License 2.0.
ctc
change set.seed way of doing
graph
Renamed graph.(so/dll) BioC_graph.(so/dll) to avoid conflicts with graphviz.
affxparser
more mods for CHP files
Biostrings
Fixed regression (introduced back in June) causing matchPDict() to report incorrect match locations when used on a MaskedXString or XStringViews subject. Thanks to H. Jaffee for the report. Bumped version to 2.13.31
Biostrings
Two small changes in alphabetFrequency():
(1) when used with 'baseOnly=TRUE', the frequency of the gap letter ("-") is
not returned anymore (now it's treated as any 'other' letter i.e. any
non-base letter);
(2) added the 'freq' argument.
Added the dinucleotideFrequency(), trinucleotideFrequency(),
allOligonucleotideFrequency() and mkAllStrings() functions.
Renamed some files in inst/extdata/ to use the same extension (.fa) for all
FASTA files.
Version bump.
nem
Changed biocViews entry of Statistics to Bioinformatics.
Biostrings
bumped version to 2.7.32
Biostrings
Added save.XStringSet() for convenient and efficient serialization of an XStringSet object. Bumped version to 2.13.33
GGBase
improved plot_EvG
maSigPro
fixed typo in title
RpsiXML
fix bug in RpsiXMLApp vignette which fails building; adds ppiStats to suggested packages
GGBase
permitting residual exploration
changes to snpsNear for more flexibility
GGBase
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Biostrings
Minor man file edit.
Added the ability to specify quality measures for the strings when performing pairwise alignments.
gaggle
updated with workarounds for windows issues
updated to 1.7.1
Biostrings
Added a pid function for calculating various forms of percent sequence identity.
HilbertCurveDisplay
changed to Michael's event loop style
- added new functions: hilbertImage, makeRandomTestData
- added compiler directive's to switch from Oleg Sklyar's to Michael
Lawrence's style of driving the GTK+ event loop under Windows. (The
latter version still needs some debugging.)
- various minor changes
[/HilbertCurveDisplay] permanent link
Biostrings
Fixed small regression introduced at r41447. Bumped version to 2.13.36
Fixed bug in matchPDict(): the dups0 slot of the input (pdict@dups0) was not propagated to the output (MIndex object) when 'pdict' contained no duplicated patterns. Bumped version to 2.13.35
Biostrings
Added "matchLRPatterns" and "matchProbePair" methods for BStringViews objects. No version bump.
Made the "show" methods for BString, BStringViews and BStringAlign objects
"getOption('width') aware" so that the user can control the width of the
output they produce. No version bump.
xcms
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Revert yesterdays change, and bring back 1.11.20 with a version bump
graph
added note to documentation about lwd behavior in nodeRenderInfo
xcms
Adapted path in vignette to new directory structure in msdata
HEM
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
ppiStats
I have updated the depends field in the desc file
GGBase
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
pcaMethods
added missing slots to class documentation
Biostrings
added the read.gapMask() function for extracting a mask from a UCSC "gap" file
Converted the profiles slots in XStringAlign from numeric to XNumeric.
Refactored pairwiseAlignment to optimize on scoreOnly setting.
Optimized memory usage for pairwiseAlignment when scoreOnly = TRUE.
Modified the pairwiseAlignment algorithm to use less memory. It is a little slower now, but can align short reads against much larger strings.
xcms
Various fixes and improvements. Add utils.R file with various general
utilities.
Increased buffer size in findMZBoxes()
Biostrings
Added the chartr() generic function with a method for BString objects.
Methods for other types of objects (in particular for BStringViews and
BStringSet objects) will come later.
Version bump.
Versatile constructor RNAString() (resp. DNAString()) now converts from DNA
to RNA (resp. RNA to DNA) by replacing T by U (resp. U by T) instead of
trying to mimic transciption. This conversion is still performed without
copying the sequence data and thus remains very fast.
Also the semantic of comparing RNA with DNA has been changed to remain
consistent with the new semantic of RNAString() and DNAString() e.g.
RNAString("UUGAAAA-CUC-N") is considered equal to DNAString("TTGAAAA-CTC-N").
Version bumped to 2.7.26
Biostrings
Updated dependents of IRanges to reflect changes in List/ListLike classes.
xcms
helper method added for xcmsRaw.collect
added helper method for collect
fixed typo
forgot ,
export new MS/MS searching methods
Added collect to xcmsRaw to convert to xcmsFragments, for searching
NB findPeaks method doesn't alway pick up all peaks that have ms^n data on them.
Ported phenoData code from 1.13.2
Fixed a typo
Added MS/MS searching methods. searchMetlin and similarity search methods for MS/MS data.
Fixed documentation
Added dirty nasty methods to find different metabolotes in metlin XML. the collision energy, name, mode (+/-)
Added MS/MS parser for metlin XML MS/MS data
Fix call to MassSpecWavelet
flowClust
some more updates:
in C code, update YTrans when estimating lambda in M-step instead of in update_z_u() -- just increase efficiency, shouldn't bring changes to outputs
update hist method
minor changes to README, vignette, etc.
ontoTools
fix warning on grep method
affxparser
updated to Fusion 1.0.10b
Biostrings
Adding a rep method for IRanges objects.
Added rep methods for PairwiseAlignment and AlignedXStringSet objects.
Biostrings
Refactor to make score only calculations faster.
Modified show method for overlap1 and overlap2 pairwiseAlignments.
Fixed the traceback in pairwiseAlignment.
GLAD
Weights can be used for the haarseg function.
xcms
Limit number of diffrepot-boxplots, added first Unit Tests
annotate
Removed usage (or reference) to pstricks tex style in BioC vignettes.
GGBase
minor
minor
minor fixes
ok
starting class doc
LazyLoad yes
biocGraph
added a imageMap method for graph objects following the newgraph rendering API
Biostrings
Use solveUserSEW(nchar(x, type="bytes"), ...) internally instead of narrow(ncharAsIRanges(x), ...). Bumped version to 2.9.88
Partial fix to coverage to convert to usage of XRleInteger objects.
RpsiXML
I have updated the DESC and Namespace
flowClust
minor changes to split and tmixFilter man pages
added criterion function;
made changes to man pages and vignette according to Florian's suggestions about the split/Subset method (dropped the select argument, deprecated the split argument);
dropped select argument also for Subset (with signature data.frame/matrix)
Biostrings
Polished xscat() code and documentation. Version bumped to 2.11.44
affxparser
more updates for CHP files, MultiData files begun
Biostrings
Local low-level sorting C utilities are redundant with those defined in the IRanges package. Removed them and use those defined in IRanges instead. Bumped version to 2.9.69
Finished to remove the XStringList class and family (superseded by the XStringSet family).
Renamed replaceLetterAtLoc() -> replaceLetterAt() and renamed its 'loc' argument -> 'at'. Deprecated replaceLetterAtLoc(). Bumped version to 2.9.68
Added substr and substring methods for MaskedXString objects.
xcms
And another fix so that plotting an xcmsEIC obtained from an xcmsRaw works again
xcms
updated diffreport documentation
Fixed missing match.arg(value) in diffreport()
Added ... to diffreport to pass optional parameters to mt.teststat
Added value = c("into","maxo","intb") parameter to diffreport
Added warning if non-unique scantimes are detected to xcmsRaw()
findPeaks.centWave generates a warning if data seems to be not in centroid mode
Added method isCentroided()
Added prefilter option to findPeaks.centWave
Fixed bug in centWave/fitGauss
Added prefilter option to findmzROI
Speedup for findmzROI
Renamed findMZBoxes to findmzROI
Removed findMZBoxes from NAMESPACE
affxparser
Version: 1.13.5 [2008-08-09]
o BUG FIX: writeCdf() would write 'CustomSeq' units as 'Tag' units,
and vice versa. This means that *ASCII* CDFs containing such
units and converted with convertCdf() would be have an incorrect
unit type for these units. Also, unit type 'Copy Number' is
reported as "copynumber" and no longer as "unknown".
o BUG FIX: The increase of the internal buffer for reading the
'refseq' header field of ASCII CDFs that was done in v1.11.2
was mistakenly undone in v1.13.3.
o Made readCdf() recognize more unit types.
Biostrings
Changed to descriptions of pairwise alignment in vignette.
Minor man page edit.
GGBase
deal with snpMatrix update
biocGraph
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Biostrings
Moved XInteger and Views class definitions to IRanges and added XIntegerViews class.
Biostrings
Small improvements to XStringSet basic capabilities:
- added "width" and "narrow" methods for character vectors;
- added "threebands" method for character and XStringSet objects;
- improved XStringSet-class.Rd man page;
- modified PDict() constructor to use "threebands" (for XStringSet)
internally for splitting the input dict into head+tb+tail parts.
Bumped version to 2.11.28
Biostrings
Added "isEmpty", "max" and "min" methods for IRanges/NormalIRanges objects. Disabled subsetting and narrowing of NormalIRanges objects (these operations do NOT preserve normality in general). Small improvement to the "gaps" semantic and implementation.
Performance optimization of the pairwiseAlignment function.
Added more information into the XStringAlign class to provide users with better information on the alignment.
Renamed the C file containing pairwise alignment code to get it to conform to package conventions and minor cleanup edits.
Added the ability to handle affine gaps in pairwiseAlignment.
HEM
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
GeneSelector
removed some quotes from do.call(
[/GeneSelector] permanent link
xcms
Fixed TeX Math
Fixed MSn Handling in xcmsSet(method=MS1)
Biostrings
some improvements to the "views buffer" feature
Added basic support for palindrome searching (naive approach). Version bump.
VanillaICE
updated vignette. changes to viterbi and breaks arguments
VanillaICE
Made a number of changes to the VanillaICE infrastructure. The main idea was to move away from storing SNP-level data and results from the HMM in the same R object. Classes HmmSnpSet, HmmSnpCopyNumberSet, and HmmSnpCallSet are defunct. Instead, we define a parameter class for the HMM -- HmmParameter -- and a class for storing the results from the HMM -- HmmPredict. The .Rd files were removed and rewritten. plotSnp methods were also modified to accomodate the changes in the class structure. In addition, a vignette was added to describe how one may create an instance of oligoSnpSet from BeadStudio processed data. The vignette VanillaICE.Rnw was rewritten. The example data, chromosome1, was changed to an oligoSnpSet.
xcms
added METLIN XML reader URL:metlin.scripps.edu/download/MS.XML\nAdded basic ppm and ppmDev\nAdded array matching
Pipeline framework tweaks/fixes + a start at some documentation.
Biostrings
Moved the reverse generic definition and the IRanges and MaskCollection methods to the IRanges package.
Added some alignment related classes to the export list.
Moved the coverage generic definition and the IRanges and MaskCollection methods to the IRanges package.
Biostrings
Minor reog of pairwise alignment methods table.
xcms
Added error message in getEIC() to use fillPeaks() for filling up NA values
Added error message in getEIC() to use fillPeaks() for filling up NA values
Added error message in getEIC() to use fillPeaks() for filling up NA values
ppiStats
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xcms
Removed Rgraphviz Output from Vignette, which caused Bus errors on some MacOS installations
flowClust
Major update: enable K to take a vector of values, and include the option of running short EMs for random initializations
- add classes flowClustList and tmixFilterResultList
- define all the utility and plotting methods for these two classes
- include the criterion replacement method
- add optional arguments criterion, B.init, tol.init to flowClust()
- update all man pages and the vignette
- bump version to 1.7.0
NOTE: there is a mysterious bug found when defining the tmixFilterResultList class. The data part cannot be assessed directly by typing the object name; it has to be assessed through the .Data slot. Tracked down to find that it may be related to the multipleFilterResult or AssayData class it extends.
Biostrings
Sync up with changes in IRanges C interface to make the Biostrings/IRanges C interfaces usable in C++ code. Bumped version to 2.9.90
rbsurv
Changed biocViews entry of Statistics to Bioinformatics.
SLGI
Moved org package to suggests, moved Biostrings to suggests, moved GO.db to imports and suggests to tidy up package dependencies.
graph
fixed updateGraph, it can now also update object from before graphData times
Biostrings
Finished adding code to support the endGap argument to pairwiseAlignment.
Added an endGap argument to pairwiseAlignment to allow users to ignore end gaps when performing pairwise alignments.
GGBase
Changed biocViews DNACopyNumber to CopyNumberVariants and SNPsAndGeneticVariability to SNP, GeneticVariability.
Biostrings
Minor doc change.
GLAD
Fixed image key in arrayPlot.arrayCGH() function. This was causing problems for the MANOR package.
ppiStats
i have added the separateExptBySize func
VanillaICE
fixed bug in calculateCnSE function
added a few comments in the vignette regarding AnnotatedDataFrame objects for featureData -- column labels position and chromosome are important
affylmGUI
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
keggorth
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowClust
Major update: enable K to take a vector of values, and include the option of running short EMs for random initializations
- add classes flowClustList and tmixFilterResultList
- define all the utility and plotting methods for these two classes
- include the criterion replacement method
- add optional arguments criterion, B.init, tol.init to flowClust()
- update all man pages and the vignette
- bump version to 1.7.0
NOTE: there is a mysterious bug found when defining the tmixFilterResultList class. The data part cannot be assessed directly by typing the object name; it has to be assessed through the .Data slot. Tracked down to find that it may be related to the multipleFilterResult or AssayData class it extends.
Biostrings
Small improvements to the "toComplex" method for DNAString objects. Got rid of almost all the [TODO] tags (only 3 left) in the documentation of the package and improved it quite a bit in many places.
Completed man page for XStringSet objects. Bumped version to 2.9.61
Completed man page for injectHardMask().
Added predefined RNA_GENETIC_CODE object and completed man pages for IUPAC_CODE_MAP and GENETIC_CODE.
miRNApath
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xcms
changed the PrecursorMz and PrecursorIntensity from atoi to atof which now returns a double and hence gives us accurate mass on the precursor for mzData files
affylmGUI
Changed biocViews entry of Statistics to Bioinformatics.
flowClust
code beautification and fixes for flowCore integration
GLAD
Tout est en C dans MoveBkp
graph
added a (non-exported) helper function 'updateFolder' which updates all serialized graph objects (i.e., the rda files) in a folder
nem
New Bayesnet estimator. Several Bugfixes.
SSPA
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
annotate
Added a function getQuery4TR() that allows people to create links to the TAIR website using TAIR accession numbers.
SLGI
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
GGBase
bad table name in man removed
fix table name
needed to update the sqlite for annotation to include offsets and version 23a contents
Agi4x44PreProcess
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/Agi4x44PreProcess] permanent link
ontoTools
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
pcaMethods
added missing slots to class documentation
BCRANK
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
flowClust
added criterion function;
made changes to man pages and vignette according to Florian's suggestions about the split/Subset method (dropped the select argument, deprecated the split argument);
dropped select argument also for Subset (with signature data.frame/matrix)
xcms
xcmsProtoGenProfileBase -> xcmsProtoGenProfileGeneric
Replace setProtocolClass invocation with setProtocol.
RpsiXML
version bumping
graphSpeciesConverter using revInciMat intead of inciMat
xcms
fixed bug which caused segfault when compiled with gcc >4.1
ppiStats
I have created the function estimatePPIErrorRates.R based on Li and Robert's code. The PPI GS is added to
this package as well
GLAD
version 2.3.0
ersion 2.2.8
BGmix
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xcms
Fix handling of single-factor designs in xcmsSet().
Do not add a 'class' variable when setting phenoData.
Remove 'name' generic (too generic), replace with 'role' for stages and
'method' for protocols, which is just a rename of 'methodName'.
Also working on a fix for fillPeaks/getEIC where the raw pipeline should
produce an xcmsRaw (not an xcmsPeaks or anything else). This has
involved completely changing the semantics of the 'pipeline' method on
xcmsPipeline.
Warning: this commit is not tested - just getting the code out there.
some xcmsPeaks fixes
VanillaICE
viterbi algorith is in C -- significantly faster hidden markov model. faster R function for finding breakpoints from a matrix of predictions
xcms
added group.mzClust example
flowClust
when K takes a vector of values, hier clustering needs to be applied only once since the classification tree is the same for all values of K
annotate
dropped one more place the hgu95av2 was being called
Biostrings
Removing accidental check in.
TypeInfo
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
RpsiXML
I ammended the author list
BCRANK
documantation updated
xcms
Remove tabs and inserted space as per bioconductor rules :)
updated and removed bugs from simSearch method.
Optimized metlin to list method. Runs faster and reduced memory size
added rawMat() RUnit-Test.
GGBase
fixes
bug in [-smlSet
fix dropped arg
small snp set support
xcms
trying to fix Windows compilation
NAMESPACE hack to remove warning when xcms is loaded
moved Rgraphviz from required to suggested packages
Preparations for parallel peak picking using MPI, added the modified papply() function
SMAP
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
ppiStats
i have started a file containing functions to generate summary statistics
ctc
fixed Rd parser warnings
Biostrings
To the pairwiseAlignment function:
1) Added a scoreOnly parameter for returning just the score (and not that alignment).
2) Renamed matchScoring parameter to substitutionMatrix.
miRNApath
Committing the DESCRIPTION file, apparently missed it during the last commit operation.
xcms
Fix rawMat method when specific scan range specified. Fix naming of
parameters in plotRaw docs.
Fixed: "diffreport()" fails if "sortpval" is false and "eicmax" > 0, reported by Hendrik Weisser
Fixed: "diffreport()" fails if "sortpval" is false and "eicmax" > 0, reported by Hendrik Weisser
GLAD
version 2.2.0
Biostrings
Moved all matchprobes functions (except combineAffyBatch) to Biostrings
and deprecated them (also modified their man pages to show how to use
Biostrings native functions to reproduce similar functionalities).
Still need to deal with the (now broken) matchprobes vignette and a few
extra things in the package that need a new home too (most likely
Biostrings, at least for now). Bumped Biostrings version to 2.11.27
Biostrings
Added a trimLRPatterns function to allow for trimming on the flanks of XString and XStringSet objects.
Added support for indels in the left and right patterns of matchLRPatterns.
siggenes
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
RPA
Added package RPA to svn
Biostrings
Vectorized pairwiseAlignment for faster computations. This resulted in transforming AlignedXString class to AlignedXStringSet.
xcms
findPeaks.centWave:?\194?\160fixed?\194?\160missing?\194?\160mzCenter.*?\194?\160assignment,?\194?\160when?\194?\160fitgauss=T?\194?\160is?\194?\160used
rbsurv
Removed usage (or reference) to pstricks tex style in BioC vignettes.
xcms
Change NULLs in xcmsRaw prototype to empty vectors, so that a valid
object is constructed.
Replace image.xcmsRaw with an S4 method for image.
Add a simple show method for xcmsPeaks.
Add rawMat method for xcmsRaw (which returns the same thing plotRaw
did) and base plotRaw on rawMat().
Fix profile matrix function finding when xcms is imported into the
namespace of another package (added match.profFun utility which
besides simplifying the code makes match.fun work by getting it to
search a frame in the xcms namespace for .profFunctions).
GLAD
chrBreakpoint est fait en C lorque HaarSeg est utilis?\195?\169 pour la segmentation
Biostrings
Merged most of the latest C code reorganization and improvements from the testing branch of Biostrings [merge -r 32187:32251]. A small change to write_RoSeq_to_CachedXStringSet_elt() and write_RoSeq_to_XStringSet_elt() prototypes (part of the exposed C interface) break packages that call directly these functions (the fix is very easy though).
Adding a subjectViews function to get XStringViews for the subject of a pairwise alignment.
Added a coverage method for PairwiseAlignment objects.
Minor low-level bug fix to pairwiseAlignment utility function.
Further improvements to decrease timings of utility functions for pairwiseAlignment.
Improved the run times of a number of utility functions related to pairwiseAlignment.
RpsiXML
idConverter is now named 'inpIDMapper' in AnnotationDbi package
BCRANK
Added the new package BCRANK to the repository.
Biostrings
Added a TypedListV2 (TypedList version 2) class to replace TypedList virtual class. It separate implementation from concept and includes the usage of SimpleTypedList and CompressedTypedList virtual classes.
RpsiXML
version bumped to 1.2.1: RpsiXMLApp introduction part written
xcms
Fix the Calculation of Anova values for >2 sample classes, Fix polarity stuff
Added Citations
GLAD
ajout ylim dans la doc de plotProfile
Biostrings
Fixed a performance issue in "reverseComplement" methods for DNAStringSet/RNAStringSet/XStringViews that was introduced during the recent move of the "reverse" generic (+ some methods) to the IRanges package. Bumped version to 2.9.70
HilbertCurveDisplay
corrected ReadAligned -> AlignedRead
added README file for building the vignette
clean-up in vignette dir, spell check done
added vignette and other stuff
[/HilbertCurveDisplay] permanent link
nem
Updates. Added function "quicknem".
Biostrings
Added the coverage() generic function with methods for IRanges, MaskCollection, XStringViews, MaskedXString and MIndex objects. Version bumped to 2.9.2
Changed the algorithm in pairwiseAlignment to start at the end of the strings rather than the beginning to make it easier to get the scores based on alignment starts.
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.
maSigPro
Fixed typos in maSigPro.Rd adn edesign.abiotic.Rd.
Bumped up version number to 1.17.1
xcms
Import current ramp parser from sashimi svn
annotate
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
timecourse
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
syslibGTK
added missing "#ifndef MSWINDOWS" around "#include
flowClust
fixed (back) the problem of deallocation of PrecisionTmp
Biostrings
Some reformatting of man/XStringViews-class.Rd
Use the new Views() interface.
Bumped version to 2.11.52
xcms
version bump
Add clean target to remove objects created during build / INSTALL
Fixed bug in findmzROI associated with empty scans
RpsiXML
version bump to 1.2.0, vignette debugged and all dependencies are now further constrained by version number
namespace unload order changed
temporary fix of bug with psimi25Hypergraph initialization, exact reason needs to be identified
version bumping: 1.1.27 solves the bug of translateID raised by Ramona Schmid, thanks
maSigPro
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GGBase
passing check
affxparser
more changes to the CHP parsing
Biostrings
fixed a regression in "[[" for XStringSet objects that was introduced in r33688
Minor code edit.
Implemented a better method for finding the unique letters when the codec is null.
Minor refactor of alignment code to make extension easier.
Minor change to vignette example code.
xcms
Setting examples for internal functions to dontrun
More documentation work, other cleanup.
Fix in plot(eic) for xcmsEIC with absent groups
xcms
missed ramp.h
missed ramp_base64.h
Restored some (most?) xcmsFragments functionality
Promote stable 1.12.1 to 1.13.3
Version Bump just before resurrection of xcms-1.12.1
timecourse
Removed usage (or reference) to pstricks tex style in BioC vignettes.
biocGraph
fixing broken vignette
pcaMethods
Changed biocViews entry of Statistics to Bioinformatics.
Biostrings
A long due change (better late than never): renamed the 'freq'
argument 'as.prob' in the following functions:
alphabetFrequency
oligonucleotideFrequency
dinucleotideFrequency
trinucleotideFrequency
oligonucleotideTransitions
nucleotideFrequencyAt
consensusMatrix
For backward compatibility, 'freq' is still accepted but a warning
is issued if it's used (this will be removed during Biostrings 2.15
devel cycle).
Bumped version to 2.13.10
[merge -r 39724:39725 from release version]
Put call to pairwiseAlignment() in an "interactive() block" in man page
for matchPattern(). This is to avoid the 'R CMD check' failure we get on
our Windows build machines because the 733.5 Mb of memory needed by this
call cannot be allocated.
Removed "length" method for XString objects (no need to override "length" method for XSequence objects).
Biostrings
- Another set of small improvements to the matchPDict() internals (cleaner
code only).
- Bumped version to 2.11.12
affxparser
added code for legacy genotyping arrays
mostly working on the Resequencing arrays
fixed a couple of bugs in the CHP parsing code
more mods for CHP files
pcaMethods
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
sizepower
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
- added file for testing the class DNAString (only tests for subsetting
for now )
- trying to fix further the unit tests
- Added section at the bottom of TODO list
- first attempt at fixing existing broken unit tests
Biostrings
Added a pid function for calculating various forms of percent sequence identity.
Fixed the reference section of the help file.
Biostrings
Mostly addressing some S4 problems triggered by a recent change
in R (https://stat.ethz.ch/pipermail/r-devel/2009-March/052824.html):
in short, removing the "initialize" method for A objects will ensure
that new("A") will always work which seems to make setClass() happier
when trying to extend A.
While making this change, I also discovered that the objects returned
by pairwiseAlignment() were invalid PairwiseAlignedXStringSet or
PairwiseAlignedFixedSubject instances so I ended up making a few
additional changes.
o QualityScaledXStringSet class:
- Made it contain the XStringSet class.
- Fixed typo in validity method.
o AlignedXStringSet and QualityAlignedXStringSet classes:
- Changeg the definitions of these 2 classes to address a design
problem when having the latter containing the former. See
NOTE at beginning of R/AlignedXStringSet-class.R for the details.
In addition, the constraint that the 'unaligned' slot must be a
QualityScaledXStringSet object is now part of the definition of
the QualityAlignedXStringSet class.
- Got rid of the "initialize" methods for AlignedXStringSet and
QualityAlignedXStringSet objects. The extra logic they were
providing (type checking) is better handled via validity methods.
- Small modification to "[" for AlignedXStringSet objects so that it
works on QualityAlignedXStringSet objects too. The "[" method for
QualityAlignedXStringSet objects is not needed anymore.
- Added a FIXME comment to .valid.QualityAlignedXStringSet().
o PairwiseAlignedXStringSet and PairwiseAlignedFixedSubject:
- Got rid of "initialize" methods for PairwiseAlignedXStringSet and
PairwiseAlignedFixedSubject objects.
- Removed validity method for PairwiseAlignedFixedSubject objects:
was redundant with validity method for PairwiseAlignedXStringSet
objects.
Bumped verion to 2.11.45
GGBase
add snpdepth class to disambiguate!
added class export filteredMultiGw..
xcms
also check ramp status
prepare for some ramp work
findPeaks.centWave: ROI detection was rewritten,
new version is faster and needs less memory,
some small bugs were fixed
findPeaks.centWave gains an optional argument "noise",
which is useful for data that was centroided without any intensity threshold,
centroids with intensity < "noise" are omitted from ROI detection
Added function rawMz()
ontoTools
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
GGBase
links in doc to GGtools
maSigPro
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
syslibGTK
initial submit for syslibGTK. Most of the codes has been taken from HilbertVisGUI.
siggenes
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
nem
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GGBase
passing check
bump
new doc
affxparser
Version: 1.11.3 [2007-12-01]
o Removed argument 'reorder' from readCel() and readCelUnits()
since its name was misleading (the returned value was identical
regardless of 'reorder', but the reading speed was faster when
'reorder' was TRUE, which is how it is now hardwired).
Biostrings
Removed local Dups class and use Dups class from the IRanges package.
Added vwhichPDict() (not yet optimized). Also whichPDict() now returns the pattern indices in ascending order.
GLAD
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Dropping the version number so it will be bumped to 2.0.0 later.
ajout de l'algo HaarSeg
ajout de l'algo HaarSeg
dyebias
changed citation details
title change, and citation details
date
bumped version number to reflect changes (mostly to do with better handling
of difference between plain marray and our own marrayExt).
CoCiteStats
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Biostrings
version bumped to 2.7.34
Biostrings
Added "reverse" method for character objects and deprecated strrev() in its favor.
Moved oligonucleotideFrequency() and related functions to its own man page.
oligonucleotideFrequency(): implementation is now entirely in C (except argument checking). Bumped version to 2.11.55
SSPA
Bumping the version number for the upcoming release.
xcms
Use the recently added Rzlib library in R-devel on Windows.
Biostrings
Minor refactor to make it easier to loop over strings in the future.
biocGraph
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
annotate
Updating a slightly outdated chromLocation object.
ppiStats
changed depends field and bumped version
SLGI
Removed usage (or reference) to pstricks tex style in BioC vignettes.
rbsurv
Updating subversion
prism
Remove unused BioConductor build options file.
Biostrings
Removing calculation of alignment profile since its cost outweighs its benefits.
Biostrings
Added utility functions alloc_XStringSet() and write_RoSeq_to_XStringSet_elt() (part of the C interface) for creating an XStringSet instance in 2 steps: first create the skeleton (with junk data in it), then fill it with some input character data (typically read from a file). Version bumped to 2.7.36
RNAseq
starting RNAseq package
GLAD
changement de l'adresse email
xcms
Added group(method=mzAlign), fixes in pipeline stuff
RpsiXML
organisms are separated by commas
bugfix: complex 'show' method did not print the interactor number properly
annotate
Updates the useHomology vignette.
This replaces the useHomology vignette with a small vignette that
describes how to use the newer inparanoid homology packages.
Backed hsahomology and xlahomology out of Depends field in DESCRIPTION file.
SMAP
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GGBase
collate fix
bugfix -- add isCis condition for plotting gene position in cwSnpScreen plot
GeneSelector
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/GeneSelector] permanent link
Agi4x44PreProcess
ddNORM$R, $Gb and $Rb have been set to ddNORM$G to avoid dimensionality problems in other functions. In ddNORM, the only field that is useful is the $G. here is where the normalized signal is stored.
changed nARR=dim(RGlist)[2] for nARR=dim(RGlist$G)[2]
Correction in BGandNorm.R, options for BG and NORM. Outpuut is RGlist$G in log2 scale. The rest of the fields, RGlist$R, $Gb and $Rb are set to NULL
[/Agi4x44PreProcess] permanent link
xcms
fixed .Rd error
affxparser
Version; 1.11.6 [2008-03-04]
o Add ability to parse PGF and CLF files
HEM
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
Added the read.liftMask() function for reading a mask of "inter-contig gaps" from an UCSC "lift" file. No version bump.
Fixed the profile calculation method in pairwiseAlignment.
xcms
Adding Steffen as a package author
Fixing a couple coding/documentation bugs in plotTIC
preprocessCore
(1.7.5) Fix bug when scale estimate provided to rcModelPLM()
[/preprocessCore] permanent link
VanillaICE
updated how transition probabilities are passed to the viterbi. store emission probabilities in an array for HmmParameter
gaggle
updated maintainer information
xcms
added group.mzClust example
fixed docu mismatch
GeneSelector
Bumped the version number to prepare for BioC 2.2 release.
[/GeneSelector] permanent link
DynDoc
Updating the license reference to reflect R standards.
flowClust
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xcms
Added polarity selection to xcmsSet
added split.xcmsRaw
syslibGTK
more stuff in vignette
Started writing a vignette
xcms
Fixed xcmsFragments manpage
flowClust
fixing a minor issue with the conversion to multipleFilterResults and also a documentation glitch
dyebias
submitted -> in press
Added package dyebias to the repository
flowClust
update README instructions for Windows users
minor change to Makevars.win
Biostrings
Implemented the quality-based substitution matrix method of Ketil Malde.
DEDS
Minor change to vignette to get around MiKTeX bug on Windows.
flowClust
small fix to hist() method for subsetting when the object is one-dimensional
xcms
initializing variable, which windows and macos complain about
VanillaICE
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GGBase
update to pass check
annotate
Fix to htmlpage(). The repository is supposed to be a list, and this is what is claimed in the help page, but the default was a character vector. The default is now list(ll).
ppiStats
fixed typo in DESCRIPTION file
affxparser
Fixed the CDF header bug: line 723 and 724 has the number 65000 changed to 400000
Updated to Fusion SDK 1.11
ppiStats
and bumped the version number
fixed the license, the description and the exports
Biostrings
Fixed a bug in mismatchSummary for AlignedXStringSet objects.
Moved calculation of nmatch for PairwiseAlignment objects down to C.
Modified coverage method for PairwiseAlignmentSummary to make it more efficient when start and end aren't supplied.
GLAD
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Biostrings
More work on the PDict() constructor (now supports almost all kind of Trusted Band dictionaries, not only Trusted Prefix dictionaries, cropping the input sequences via the tb.start/tb.end/tb.width args is almost fully implemented). matchPDict() not yet ready to accept PDict objects with a head. Renamed the ULdna_PDict class -> CWdna_PDict. Version bumped to 2.7.24.
More work on the PDict() constructor (changed its signature, the length of the Trusted Dictionary must now be specified via the 'tb.width' arg instead of the 'tb.end' arg). Version bumped to 2.7.23.
pcaMethods
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
biocGraph
updated the dependency on hgu95av2 to hgu95av2.db
ppiStats
updates to estimateCCMErrorRates.R
xcms
Fixed lack of scan error
Biostrings
Fixed bugs causing p2nmatch() and extractAllMatches() to fail when no match were found. Version bump.
affxparser
Version: 1.13.7 [2008-08-23]
o SPEED UP: readCcg() is substantially faster after removing
all gc() calls.
Version: 1.13.6 [2008-08-21]
o Updated Fusion SDK from 1.0.10b (Jan 2008) to 1.0.11 (July 2008).
GGBase
phenoVar alias needed
xcms
Not fully finished, but added some of the new slots for MSn
added collision energy to rampRawDataMSn method
Added collision energy slot
Bumped dependency for MassSpecWavelet, which now has local Noise estimation (and API changes)
Biostrings
Fixed an integer overflow issue for TypedList by replacing elementCumLengths slot with elementLengths slot.
Rdbi
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
xcms
suggest: msdata package for vignette
added fillPeaks.mean
Updating installation documentation with BioC Softare repository
BCRANK
fixed match.length warning
RpsiXML
changelog
Version 0.0.2: Passing R-2.7.0 and R-2.8.0-devel checking without warning or noting
Syntax change: pairvec in iListHandler and curEL in eListHander are assigned with a foo value to avoid the warning of invisible global variable binding
Bumping the version number
Trivial change: warning under R-2.8.0-dev removed by importing generic function definition 'abstract' from Biobase package. It does not work so far since i got a tippfehler, sorry
Biostrings
Fixed a pairwiseAlignment quality-adjusted scoring bug that was introduced when moved to XStringSet.
annotate
deprecated and defuncted some old functions.
These functions don't appear to be used anywhere else (I checked).
Also, they are long overdue for this.
graph
fixed Rd version 2 parser warnings
ontoTools
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
miRNApath
Version 1.1.3, fixed miRNA-gene counts code and strategy for ignoring pathways with no hits.
SLGI
fixed Rd issues found by Rdversion 2 parser
xcms
change from doubleMatrix() to double()
Fix duplicate setGeneric()
Biostrings
Fixed some bugs in trimLRPatterns and added support for ragged length subjects when using Rpattern.
Biostrings
Simplify argument specification.
Fixed typo in code.
Change tie breaking for trimLRPatterns from least aggressive to most aggressive trimming.
xcms
Fix for Tandem-MS files without MS1
Biostrings
cosmetic
- Added the intToIntervals(), intToAdjacentIntervals() and narrow() functions for
creating or modifying IntIntervals objects. Those functions together with the
restrict() function added previously are used by the BStringList() and BStringSet()
constructors and family.
- Fixed a nasty bug in the narrow_BStringList() C function.
- Some additions and improvements at the C level.
- No version bump yet.
TypeInfo
Replaced reference to soon to be defunct class exprSet with ExpressionSet in test script.
xcms
findPeaks.MSW is compatible with patched versions of MassSpecWavelet
xcms
Fixed legend in obiwarp plots, fixed documentation
Remove unneccessary scaling in deviation plot
of retcor(method="obiwarp")
Renamed obiwarp parameters
GGBase
ok
pcaMethods
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
gaggle
updated description
moved classpath fix to correct location
fixed classpath issue
hypergraph
A recent modification in methods::setClass() requires that new("A")
must work for A to be extendable.
I modified the "initialize" method for Hypergraph objects in order
to satisfy this new requirement. Now 'new("Hypergraph")' works (and
Rintact and RpsiXML packages can extend Hypergraph.
Bumped version to 1.15.2
Biostrings
Added the "palindromeArmLength", "palindromeLeftArm" and "palindromeRightArm" generics and methods. Added a man page for all the palindrome related functions.
some improvements to the "views buffer" feature
limmaGUI
change double dashes to single dash
changes on dashes to ordinary ones
GGBase
minor fix to sym2pid
DEDS
Minor change to vignette to get around MiKTeX bug on Windows.
VanillaICE
check in sweave
xcms
Revert to r32093 fixing the plot(eic) bug
GGBase
ok
need illuminav1
doc to pass check
ok
various shims to deal with alterations to snpMatrix
Biostrings
Added a quality method for numeric error probabilities.
RpsiXML
I updated the Description file as per Marc's suggestion
graph
fixed a bug
VanillaICE
removed whitespace from \item{value} { in transitionScale.Rd
SLGI
set to dependence the org.Sc.sgd.db package and modify man page so the check time should be shorten
Biostrings
Added the Twobit and Twobit_PDict classes for supporting a new type of preprocessing: for a Twobit_PDict object, the 2bit-per-letter signature of each DNA sequence in the Trusted Band is preprocessed and the mapping from the signatures to the position of the sequences (in the Trusted Band) is stored in the object in a form that allows very fast lookup. One important limitation of this approach though is that the width of the Trusted Band must stay relatively small (currently <= 14). Also added support for Twobit_PDict objects in matchPDict()/countPDict(). Some preliminary testing seems to indicate that, in some situations, matchPDict()/countPDict() could be more than 2x or 3x faster on a PDict object of type "Twobit" than on one of type "ACtree" (still need to do more testing though). Version bumped to 2.9.29
affxparser
Version: 1.17.3 [2009-05-29]
o Added applyCdfGroupFields() and cdfSetDimension().
Version: 1.17.2 [2009-02-20]
o BUG FIX: readChp() would crash (segmentation fault) for (at least)
some CHP files for GenomeWideSNP_5 generated by Affymetrix Power Tools.
o BUG FIX: Updated compareCels() to work with new readCelHeader().
Version: 1.17.1 [2009-05-09]
o Now readCelHeader() also reads DAT headers from Calvin CEL files.
Version: 1.17.0 [2009-04-20]
o Devel version bumped because of the new Bioconductor release.
Version: 1.16.0 [2009-04-20]
o Release version bumped because of the new Bioconductor release.
Biostrings
Added basic support in matchPDict() for inexact matching of a dictionary with "trusted prefixes". See ?`matchPDict-inexact` for the details. There has been lots of renaming related to the matchPDict() stuff since 2.7.16, sorry. Version bump.
oops
HilbertCurveDisplay
Adding a new HilbertCurveDisplay empty package for Simon Anders
[/HilbertCurveDisplay] permanent link
nem
Updates:
- Added new Method Generalized Nested Effects Models (GNEMs)
- Common way to set Parameters
- Sahin dataset
- Added NAMESPACE
- Bugfixes
annotate
some extras
graph
When setting edge attributes via edgeRenderInfo on undirected graphs the order of head and tail nodes in the node names is ignored, i.e. a~b is equivalent to b~a
Biostrings
Allow users to specify integer, numeric, character, BString, and BStringSet objects as quality measures to the pairwiseAlignment function.
VanillaICE
check for zeros in copy number when computing emission probabilities
DEDS
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
pcaMethods
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
RpsiXML
Release 1.5.19: typedList class has been replaced by the simple 'list' object, which reduces the parsing time by 33%. See the NEWS for details.
spelling error removed
annotate
Minor change in vignette text to reflect changes that were made to example code introduced in Revisions 16330, 23990, and 27757.
xcms
Add some symbols to the namespace.
affylmGUI
Replaced support for defunct class exprSet with ExpressionSet.
HEM
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
TypeInfo
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
annotate
updating a bit, removing empty parts in man pages, moving xtable to be
an import, not a depends
GGBase
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
xcms
Fix obiwarp builds without cmdparser.o
Biostrings
Fixed bug in mismatch slot creation when generating *PairwiseAlignment from strings.
Reworking of IRanges TypedList-derived classes. If appropriate, the data in these TypedList classes can be compressed down to a single list element to save space. This had ripple effects to the Biostrings package and the pairwiseAlignment functionality.
hypergraph
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
sizepower
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
ppiStats
i am checking in man page i forgot to do
RpsiXML
I have modified the depends and import in the DESC and NS...this still might need to be updated
SLGI
bump version number for Bioc2.2 release
Biostrings
Added the vmatchPattern() generic function with a method for XStringSet
objects. vmatchPattern()/vcountPattern() are the vectorized versions of
matchPattern()/countPattern() i.e. the subject must be an XStringSet
object (support for XStringViews objects will follow soon).
Bumped version to 2.11.2
VanillaICE
changed licence in the description to LGPL
SLGI
dSLAM data update
timecourse
Replaced support for soon to be defunct class exprSet with ExpressionSet.
Biostrings
Added headers for R math and random number generation.
Temporarily reverting back to r40103.
siggenes
Added a few new functions for further extensions of SAM and EBAM.
part2
part 1 of the always lovely fun with renewing the description file.
annotate
Changed default repository in htmlpage() from 'll' to
DynDoc
fix mismatches from documentation object 'getPkgVigList'
Biostrings
Minor corrections to vignette.
Removed the row names from the show method for summarized pairwise alignments.
fixed a typo
Slight change to prepositional phrase.
Minor tweaks to man pages.
Added references to Needleman - Wunsch and Smith - Waterman papers.
HilbertCurveDisplay
corrected setting of PKG_CONFIG_PATH
(use :=, not =, and ;, not :)
[/HilbertCurveDisplay] permanent link
rbsurv
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
Biostrings
Further optimization of slice function.
Minor refactor to slice to make it more efficient.
Minor code fix to slice function.
Added a slice function for generating IRanges from coverage calculations.
Renamed whichRanges to whichAsRanges.
Added a whichRanges function that behaves like the which function, only it returns IRanges rather than integers.
[merge -r 32471:32660 from the testing branch of Biostrings] This merge from the testing branch introduces support of MTB_PDict objects (Multiple Trusted Band PDict objects) which can be used with matchPDict() for performing inexact matching with a small number of mismatching letters at any position in the individual patterns of the original dictionary. It also introduces the new "whichPDict" generic.
Biostrings
Added the read.rmMask() and read.trfMask() functions for reading a mask from a RepeatMasker .out file or from a Tandem Repeats Finder .bed file. No version bump yet.
Added score profiles to pairwiseAligment results to allow users to see how well strings align at different points.
ppiStats
Added AnnotationDbi and methods to Depends field.
xcms
added plotting options to plot.metlin
Biostrings
Removing unneeded spaces in usage section.
Renamed PWMscore() -> PWMscoreStartingAt() (thru PWMscore deprecation) for more consistent naming with other *At() functions (e.g. neditStartingAt()).
Renamed pairwiseAlignment types subjectOverlap to global-local and patternOverlap to local-global to reflect names commonly used by other systems. Issue warnings in pairwiseAlignment and stringDist when the old names are used.
Made the coverage method for MIndex objects use the underlying code for IRanges and added gapCode arguments to aligned and consensusMatrix methods for pairwise alignment objects.
xcms
Changed to allow for method change :)
Added score_fun methods
Added score_fun method choices
Biostrings
Arghh, a typo broke 2.7.19! Fixed now (and version bumped to 2.7.20).
Updated inst/NEWS and bumped version to 2.7.19.
Biostrings
added 'verbose' arg to save.XStringSet()
Biostrings
Refactored pairwiseAlignment to make it easier to obtain mismatch information. This involved added an additional slot to PairwiseAlignment objects and created mismatch methods for AlignedXStringSet and PairwiseAlignment objects.
Also renamed indels to indel.
xcms
Fixed : plotTIC won't work if object@tic slot is empty
xcmsSet() now gives an error message if no data files were found
docu updates & fixes
More straightforward API for findPeaks.centWave, much less parameters are needed
CAVE: peak width range (in seconds) is used instead of scale range
CAVE: ppm instead of dev parameter
xcms
Fixed xcmsBoxPlot()
affylmGUI
Remove some corrections by P. Aboyoun in main.R. The references to exprSet are needed
to check old data files for class name of exprSet and if present retrieve data from them
without needing the exprSet class definition.
also reformat the layout of some code to my liking.
This version ready for release with Bioconductor 2.2
Change references back to exprSet to allow loading of old data files, without using exprSet objects
Reformatting some code
siggenes
Now full gene names can be added to the html output.
Biostrings
Fixed serious memory corruption bug in the C code in charge of low-level manipulation of the extendable buffers (thanks Martin for finding this one). Bumped version to 2.7.35.
GLAD
version 2.2.7
xcms
Fixed split() and c() for xcmsSet
Biostrings
Refactored how quality scores are represented in the pairwise alignment process through the use of the QualityScaledXString class.
Fixed a bug in mismatchTable when shiftRight > 0 and unaligned is a single string.
Changed indel slot in AlignedXStringSet to use a RangesCollection instance.
xcms
Modified all target in Makevars to delete old object files to support usage on Mac OS X.
Correctly parse Bruker MS2 precursor masses
xcms
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
DEDS
fixed Rd parser warnings
affylmGUI
Added GUI to DESCRIPTION file.
SLGI
Added lattice and methods to the Depends field.
BCRANK
penalties P1 and P2 are now optional
GeneSelector
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/GeneSelector] permanent link
miRNApath
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biostrings
typo
xcms
Fix includeMSn handling in xcmsSet + Graphviz fix + use filepath for CDF path
Biostrings
Minor improvement to maskMotif(). Updated some of the examples dealing with masks. Bumped version to 2.9.80
Updating NEWS file to reflect recent changes.
use names() instead of desc() on XStringSet/XStringViews objects, internally and in the examples
Added a consensusString function.
annotate
minor addition to list
xcms
Fix a few bugs in the pipeline framework. Add profileMatrix<- for
setting a pre-generated profile matrix on an xcmsRaw.
changed the PrecursorMz and PrecursorIntensity from atoi to atof which now returns a double and hence gives us accurate mass on the precursor for mzData files
annotate
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
SSPA
Added package SSPA to the repository
xcms
xcms allocates a lot less memory when loaded
workaround for openSUSE 11.0 gcc compiler bug
siggenes
Added function for performing SAM and EBAM to test for linear trend in ordinal data (with, e.g., Cochran-Armitage trend test).
rbsurv
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
Biostrings
Fixed url link in man page.
Biostrings
- Fixed a regression introduced in version 2.11.12 when using matchPDict() on
a PDict object with a head or a tail (i.e. with a Trusted Band not covering
the entire dictionary).
- More work on the ACtree2 container.
- Bumped version to 2.11.15
GGBase
ok
minor
minor
graph
fixing docs
RpsiXML
Creating a new package directory for Tony Chiang and Jitao "David" Zhang.
HilbertCurveDisplay
corrected version number
corrected license
Note added to INSTALL
various clean-up
[/HilbertCurveDisplay] permanent link
Biostrings
Added the "alphabet" method for "XStringSet" objects + a few additions to the TODO file. Version bumped to 2.7.42.
Biostrings
Added new XStringQuality classes to make it easier to manage string quality information.
siggenes
Two small bugs fixed.
SMAP
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowClust
Changed biocViews entry of Statistics to Bioinformatics.
VanillaICE
fixed bug in the viterbi wrapper. fixed a few plotting bugs in the vignette
SLGI
Add packages PCpheno, SLGI to bioc-devel
xcms
Fix splitting of xcmsSets with samples without peaks
Add tests for Splitting single/no sample from xcmsSet
VanillaICE
export genotypeEmissionCrlmm
fixed bug in genotypeEmissionCrlmm
updated emission function
modified function for calculating emission probabilities. added genotypeEmissionCrlmm that incorporates confidence estimates of crlmm genotype calls -- only works for affy6.0
Biostrings
cosmetic
GGBase
added class export filteredMultiGw..
added filteredMultiGwSnpScreenResult
filteredGwSnpScreenResult class added
some basics
Biostrings
Location of CL2001032020AA.cel file has changed.
Some adjustments to list-like classes MIndex and XStringSet. Made PDict a list-like class too. Bumped version to 2.11.36
GLAD
aws remplac?\195?\169 en Suggest
ajout de trace dans le configure
RpsiXML
Licence: The package is now released under LGPL >= 2
Documentation: supporting information for MatrixDB added
xcms
check for successful buffer allocation
dyebias
made up to date with respect to latest UMC version (rev 3396, Mon May 25 13:29:21 UTC 2009)
GLAD
derni?\195?\168res optimisations
GGBase
minor syntax in Rd
graph
making sure that the edgeRenderInfo for arrowhead and arrowtail is reset when changing the edgemode of a graph
BCRANK
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
hypergraph
Fixed a matrix subscripting bug and an unlist related warning.
GLAD
ajout du NAMESPACE
Rdbi
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Biostrings
Third (and hopefully last) attempt to refactor the match reporting
facilities used by matchPDict() at the C level. This one looks good.
The design of the new code should make it easy to support storage of
matches that have a width different from the width of the pattern
they derive from (this will happen when matchPDict() will support
indels). Bumped version to 2.13.20
Temporarily reverting back to r40157.
Second attempt to refactor the match reporting facilities used by
matchPDict() at the C level. Code is still not ready (will revert
back in the next commit).
Resync with latest change to the "Auto-Extending buffer" code in IRanges. Bumped version to 2.13.19
Biostrings
matchPDict() now supports IUPAC ambiguities in the subject i.e. it will
treat them as wildcards when called with 'fixed=FALSE' on a Trusted Band
dict or with 'fixed=c(pattern=TRUE, subject=FALSE)' on any dict.
The implementation of this new feature uses a "split and merge pointers"
technique while walking the Aho-Corasick tree. Some testing, benchmarks,
code optimization and cleaning are still required. In particular it
needs to be tested on a genome with injected SNPs.
Version bump -> 2.7.44
Agi4x44PreProcess
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/Agi4x44PreProcess] permanent link
preprocessCore
(1.1.7) Fix background function bindings (for use by other packages). The implementation themselves is unchanged.
(1.1.6) Addition of PLM-r and PLM-d
Adjust rcModelPLM so that it takes optional row-effect estimates
quantile normalization functions normalize.quantiles(), normalization.quantiles.determine.target(),normalize.quantiles.use.target() all now have multi-threaded support, user controlled using the R_THREADS environment variable
Move weightedkerneldensity.c from affyPLM to preprocessCore
subColSummarize* functions all now have basic multi-threaded support, user controlled using the R_THREADS
[/preprocessCore] permanent link
SLGI
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
VanillaICE
changes to viterbi source code to allow different transition probabilities between states
GGBase
pedinf reader bump v
pedinf reader
minor
keggorth
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
siggenes
Back to old argument names.
xcms
Add phenoData parameter to xcmsSet, and extract to a separate
function the logic of deriving phenoData from a vector of paths. Rework
API for extracting pipeline subsets (local vs ancestry) from xcmsData
instances. Add check to profileMatrix<- to ensure histories of xcmsRaw
and xcmsProfile are compatible.
Moved Rgraphviz from Suggests to Depends field.
RpsiXML
Updated the hypergraphConverter() to allow columns to be mapped.
This just fixes something that I consider a bug, and that is that when
you pass an incidence matrix in that is genes by genes, you should be
able to map all the genes and get back an appropriate matrix.
Biostrings
minor improvements to man/letterFrequency.Rd
Added 'shift' and 'width' args to consensusMatrix() and consensusString().
Bumped version to 2.11.49
Made XStringSet_xscat() safer by catching signed integer overflow for the ans_super_length variable. Bumped version to 2.11.48
SMAP
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
RpsiXML
Updated suggests field to add annotation dependencies.
Biostrings
Completed a "release candidate" for the alignments vignette.
Checked in some answers to the adapter example in the Alignments vignette.
Begun adding exercises to removing adapters from sequence reads section.
Minor text addition to Alignment vignette.
Added exercises for protein alignment in vignette.
Added exercises on edit distances to Alignment vignette.
Added another set of exercises to the Alignment vignette.
Changed some of the examples and added exercises to the Alignment vignette.
Removed unwanted names from the nchar method for PairwiseAlignmentSummary objects.
Added content to the Computation Profiling section of the Alignments vignette.
xcms
xcmsFragments cleanup and documentation, added Rgraphviz to suggests
fixed wrong object name in xcmsSet.show()
Biostrings
Added PROTECT calls to returns of get_IRangesList_elt since it creates a new IRanges object.
Replace usage of LENGTH(GET_SLOT(ranges, install("start"))) with get_IRanges_length(ranges).
limmaGUI
Changed biocViews entry of Statistics to Bioinformatics.
xcms
Pass further parameters down to findPeaks-MSW
xcms
findPeaks.centWave: added check & warning for invalid scanrange parameter
RpsiXML
fixed man page warnings
hypergraph
Adds a convenience function to hypergraph.
New function just converts and incidence matrix into a hypergraph.
Biostrings
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Biostrings
Minor code simplification change (added usage of replaceLetterAtLoc).
GGBase
Added scanDate slot to Biobase's eSet class, added functionality in affy to utilize the new scanDate slot and updated all the packages that create direct subclasses of eSet, ExpressionSet or NChannelSet.
nem
fixed Rdversion 2 parser warnings
fixed Rdversion 2 parser warnings
RpsiXML
Bug fixes for new species to same species mapping.
This fixes some bugs the cropped up when adding the ability to map
from one species to a different ID in the same species.
GLAD
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
annotate
Swapped usage of old style deprecated annotation paradigm with new AnnotationDbi paradigm.
xcms
findPeaks.centWave: generates a warning if data seems to be not in centroid mode .. changed diff-threshold to 0.25
GLAD
fixed Rd version 2 parser warnings
Biostrings
Fixed a performance issue in "reverseComplement" methods for DNAStringSet/RNAStringSet/XStringViews that was introduced during the recent move of the "reverse" generic (+ some methods) to the IRanges package. Bumped version to 2.9.70
added early version of "sort" method for XStringSet objects
gaggle
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GLAD
optimisation de certains codes (passage en c++)
graph
can update really old graphs now from the pre-graphData era
added missing IMCAAttrs object back to the serialized graph
xcms
Pass further parameters down to findPeaks-MSW
Moved Meta-Data for MSn to xcmsRaw object and changed MSn to all-vectors
Biostrings
Added the hasOnlyBaseLetters() generic function with methods for "DNA and RNA input".
Biostrings
Minor bug fix to quality score coercion method.
Removing comment in vignette.
Minor fix to use new summary method for RangesList object in summary method for PairwiseAlignment objects.
The XStringSet class does not extend the IRanges class anymore. Now the ranges are stored in the new 'ranges' slot. Bumped version to 2.9.82
affxparser
moved the updates from release to devel
Biostrings
Added the "alphabetFrequency" and "oligonucleotideFrequency" methods for MaskedXString objects. Started completing the man page for MaskCollection.
Biostrings
Put the "Views" method for MaskedXString objects back with a warning that the masks are droppped. Bumped version to 2.9.73
Added more documentation on pairwiseAlignment function.
Added more explanation to the creation of the agrepBioC function.
Resynced with latest changes in IRanges.
Fixed "coverage" method for PairwiseAlignmentSummary objects.
Deprecated subXString() in favor of subseq().
Defuncted subBString().
Minor typo fixes.
xcms
Cleaned up Makevars to allow for parallel make during construction.
graph
noted that join() will set edgeweights to 1 in resulting graph
Biostrings
Minor refactor to speed up performance of compareStrings.
Fixed a C pointer bug in compareStrings.
Biostrings
Added N50 doc from Nicolas Delhomme (with some small tweaks). Bumped version to 2.13.24
Biostrings
Added basic support for Position Weight Matrix matching thru the new matchPWM() and countPWM() functions. Also added related utility functions maxWeights(), maxScore() and PWMscore(). See ?matchPWM for the details. Bumped version to 2.7.47.
Minor edits to the description and details section of the man file.
Disabled update() of NormalIRanges objects and fixed a small problem with the "update" method for IRanges objects.
Added "isEmpty", "max" and "min" methods for IRanges/NormalIRanges objects. Disabled subsetting and narrowing of NormalIRanges objects (these operations do NOT preserve normality in general). Small improvement to the "gaps" semantic and implementation.
affxparser
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
graph
edgemode slot is now gone
Biostrings
Added DNA_BASES and RNA_BASES constants. Made alphabet() generic again and added the dots (...) argument to it (so it can support 'baseOnly=TRUE' on DNA or RNA objects).
Completing the set of methods for matchPattern(), countPattern(), vmatchPattern(), vcountPattern(), matchPDict(), countPDict(), vmatchPDict() and vcountPDict() so that the 4 basic string containers (XString, XStringSet, XStringViews and MaskedXString) are covered. Some of them are just stubs redirecting the user to the appropriate function. Bumped version to 2.11.38
Added a set of coercion methods for turning XStringViews objects into XStringSet objects.
VanillaICE
mostly updates to add needed documentation
Biostrings
Sync up with renaming of "narrow" method for MaskCollection objects ->
"subseq" in the IRanges package. Bumped version to 2.9.91
Documented "order" and "sort" methods for XStringSet objects.
TypeInfo
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
siggenes
Updated the functions for linking genes to repositories.
Biostrings
Reverting to r31587
(I am quite confused about the tests - the API seems to
have changed since they were first written, and it is
probably better if I do not tweak them without knowing
for sure).
ppiStats
I have added a man page for the new function to partition expt data by size
xcms
Fixed MSn Handling in xcmsSet(method=MS1)
siggenes
Fixed a strange small bug.
GeneSelector
Fixed S4 class mismatches from documentation object
'GeneSelectorOutput-class': in GeneSelectorOutput-class.Rd, change the
name of a slot of GeneSelectorOutput 'rankmatrix' to 'rankings' to match
what has been coded in classes.r.
Bumped up version to 2.0.4.
[/GeneSelector] permanent link
RpsiXML
Version bumped to 1.5.3: experiment source Id is now acquired by a two-step strategy: standard and non-stardard; confidence value slot visible
Biostrings
Still need to export the "narrow", "reduce" and "gaps" methods (at least until the MaskCollection class + methods are moved to the IRanges package).
Changed pairwiseAlignment C code to reflect separation of IRanges from Biostrings.
Updated tests to reflect change in handling of aligning an empty string.
Use new_IRanges() from the IRanges C interface.
Moved the RoSeq stuff back from the IRanges package to this package (where it belongs).
Added checks for user interrupt to pairwise alignment code.
Fixed data type for pairwise alignment when one of the strings is empty.
Added const keywords in pairwiseAlignment C code to prevent inadvertent assignment.
Started to remove the IRanges stuff from the Biostrings package and to use the stuff that is defined in the new IRanges package instead. Version bumped to 2.9.55
Biostrings
Added "consensusString" method for matrices.
As a convenience, calls to BString()/DNAString()/RNAString()/AAString()
and to BStringSet()/DNAStringSet()/RNAStringSet()/AAStringSet() with no
arguments are now supported (they return a 0-letter XString object, or
an XStringSet object of length 0, respectively).
Bumped version to 2.11.46
preprocessCore
(1.7.2) Returned scale estimates are computed using residuals at last iteration rather than n-1 iteration
(1.7.1)
[/preprocessCore] permanent link
xcms
Added collision Energy support for mzData files. 26.01.08
Biostrings
Minor refactor to speed up performance of compareStrings.
Biostrings
Changed Frequency label to Probability in mismatchSummary function.
Fixed a bug in mismatchSummary when alignment is empty.
Fixed an argument check to pairwiseAlignment function.
ontoTools
Added scanDate slot to Biobase's eSet class, added functionality in affy to utilize the new scanDate slot and updated all the packages that create direct subclasses of eSet, ExpressionSet or NChannelSet.
VanillaICE
changed the default for getting confidence scores to use a robust estimate for the across sd. See calculateCnSE
fixed broken links to ParESet
Biostrings
Moved the MaskCollection class, its methods and the mask importation utilities (read.agpMask(), read.gapMask(), read.liftMask(), read.rmMask() and read.trfMask() functions) from this package to the IRanges package. Bumped version to 2.9.58
Small cosmetic improvements at the C level. Started removing the XStringList class and family (superseded by the XStringSet family).
Biostrings
Completed implementation of xscat() and added a man page. Bumped version to 2.11.43
graph
dropped a superfluous argument from some setAs defs
Biostrings
Added inst/NEWS. Version bumped to 2.7.8.
First working version of matchPDict() is ready for use. This function efficiently finds all occurences in a text (the subject) of any pattern from a set of patterns (the dictionary). See ?matchPDict for the details (especially the current limitations). Version bump will come soon.
Biostrings
A first pass at a function for generating global, local, and overlap pairwise alignments. This new pairwiseAlignment function expands on the needwunsQS function.
Replaced previous MaskedXString draft by a better design for the MaskedXString
family of containers. This is a deep change in how masking sequences is handled.
Needed to make lots of internal changes and additions in order to support this
new masking mechanism. Version bumped to 2.7.45
Biostrings
added the lettersToAmbiguity() utility function
Fixed "reduce" method for .IRanges objects and "mask" method for IRanges objects (both were broken on .IRanges/IRanges objects with names). Version bump.
Biostrings
Allow for single numeric nomatch arg, which will be converted to integer, to match method for XStringSet objects.
Created no-copy match methods for XStringSet objects.
Adding some comments to code.
Fixed the order method for XStringSet to coincide with order method in R by performing a primary qsort on value and secondary qsort on index.
Improved upon %in% method for XStringSet objects.
Fixed match function for XStringSet objects.
Minor code formatting change.
Added "%in%" and match methods for XStringSet objects.
pcaMethods
bugfix
added predict and residuals methods
siggenes
Just another bug fix (pretty exotic bug only occurring in the case of a very, very small number of samples)
Just a few bug fixes and making some output prettier.
xcms
setMethod("isCentroided", "xcmsRaw", ..)
miRNApath
fixed Rdversion 2 parser warnings
GLAD
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
ppiStats
Removed unneeded geneplotter dependency.
Biostrings
Added the PDict() constructor. The user must NOT use new("ULdna_PDict", ...) or new("TPdna_PDict", ...) anymore. Version bump.
flowClust
minor changes in flowClust.c (esp. up_data_z_weight) and BoxCox.C to increase computational efficiency;
compute output covariance matrix (sigma) in C
xcms
updated isCentroided() heuristic to work with Orbitrap/ReAdw
ppiStats
i have updated the estimatePPIErrorRates some more and will finish tomorrow
I have updated the estimatePPIErrorRates function to accept both pos and neg GS and updated the man page
ontoTools
Removed usage (or reference) to pstricks tex style in BioC vignettes.
xcms
Fix Build warnings and errors
xcms
added -DWIN32_LEAN_AND_MEAN to Makevars.win to fix ramp build on windows
xcms
corrected error report in c()
fixed calculation of specNoise for 1-point spectra
BGmix
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Biostrings
Added example using fuzzyMatrix argument in pairwiseAlignment.
pcaMethods
added kevin's biplot function and some getter functions
VanillaICE
fixed plotting of hidden states
VanillaICE
changed class definitions of HmmOptions and HmmParameter. Initialization is (hopefully) more straightforward
ontoTools
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GGBase
fixup
for cisTest
Biostrings
Switched to R's definition of negative infinity to avoid worry of overflow in order to speed up calculations in pairwiseAlignment.
Biostrings
Formally deprecated the Rle class.
GGBase
fix Rd errors
Biostrings
Added 'collapse' and 'weight' arguments to vcountPDict().
Bumped version to 2.11.54
HilbertCurveDisplay
initial check-in of HilbertCurveDiaplay, at version 0.1.2
(earlier changes in Huber group SVN)
[/HilbertCurveDisplay] permanent link
xcms
moved manpage
added retcor.obiwarp()
Biostrings
Updated the NEWS file to reflect recent changes.
Updated the coverage output for MIndex object to produce XInteger objects.
Modified coverage and slice to create XInteger and XIntegerViews respectively.
Moved function to IRanges package.
SLGI
removed whitespaces from Rd files containing /item{stuff} {
Biostrings
Fixed a bug in mismatch method for objects of class PairwiseAlignment.
Minor code cleanup to nmismatch.
Added an nmismatch function to get the number of mismatches produced by mismatch.
A couple of small cosmetic improvements to the matchPDict-exact.Rd and matchPDict-inexact.Rd man pages. Version bumped to 2.9.30
[merge -r 32437:32438 from the testing branch of Biostrings] More reorganization of the PDict class and subclasses that will make it easier to implement the upcoming MTB_PDict class (container for Multiple Trusted Band PDict objects). Lots of improvements to the PDict/matchPDict man pages.
xcms
Documentation clarification
Fix getEIC() for xcmsRaw
affylmGUI
Added LazyLoad: yes to DESCRIPTION file
Biostrings
some cosmetic changes and a version bump
Added more basic documentation of the Biostrings C interface (thru commenting Biostrings_interface.h and Biostrings_defines.h). Version bump -> 2.7.21
affylmGUI
Ensure line endings in CITATION are LF only - may have been cause of errors(unexpected end of input) on Mac OSX R CMD check
xcms
Return empty object of no peaks are found
xcms
fixed dim error on some files types
1.13.5
Parallel peak petection using Rmpi
New function xcmsPapply()
Added mpi.finalize() via .Last
Fixed some .Rd errors
Added score_fun man page
xcms
Found problem is xcmsBoxplot, fixed dim error (build sucessful :)
opps, Updated the diffreport command with height and width command :)
xcms
Added timerange paramter to rawEIC()
annotate
Fixed uncommented underscores in htmlpage documentation.
xcms
fixed documentation for findPeaks.MSW
annotate
Partial update to the useHomology Vignette.
This partially updates this vignette so that it contains more current
information. This vignette is still not ready for prime time though,
so it is temporarily remaining a .bak file.
xcms
fixed: peak parameters lmin,lmax were accidentally removed
docu fix
Biostrings
Renamed the 'mismatch' arg -> 'max.mismatch' for the matchPattern(), matchLRPatterns() and matchPDict() functions. No version bump.
Biostrings
Fixed small problem with PWMscore(), matchPWM() and countPWM(). Made extractAllMatches() work with a MaskedXString subject (masks are dropped). Added "matchProbePair" method for MaskedDNAString objects. Now use BSgenome.Dmelanogaster.UCSC.dm3 >= 1.3.7 (sequence have masks) instead of BSgenome.Dmelanogaster.FlyBase.r51 in all examples. Other small improvements to several man pages. Reorganized and updated NEWS (moved the file one level up) and TODO files. Bumped version to 2.9.20
A first pass at some simple RUnit tests for pairwiseAlignment.
Minor bug fix in aligned.
Added "reverse" methods for IRanges, NormalIRanges, MaskCollection and MaskedXString objects, and "complement" and "reverseComplement" methods for MaskedDNAString and MaskedRNAString objects.
Add vcountPattern, to count occurrend of pattern in XStringSet-derived
objects
RpsiXML
Version bumping: 0.0.3. This version added support of MatrixDB, at the same time the parsing routine is able to handle the situation where (1) one 'entrySet' has more than one 'entry' items (2) no 'interactorList' or 'interactorRef' is provided. In-line parsing of interactors are used in the second case. One open question is the problem of source ID redundancy in matrixDB, more than one source ID corresponds to one UniProt ID. Will be solved in later versions. This check-in passed R-2.8.0-devel and R-2.7.1 passing without moaning. by David
Function extension: supporting the adding of MatrixDB
Function extension: in case interactorList is not provided by the source file, now the parser will parse the in-line interactor information.
DEBUG: show method for psimi25InteractionEntry debugged for the problem of total interactor number not displayed
Function extension: support for MatrixDB added
Function extension in parsePsimi25Interactions: in case of duplicated interactors or interactions only the unique ones are returned
DEBUG: in case of only one element in entrySet, the first is returned. Checking passed
DEBUG: length(entrySet) > 1 but not >0
Function extension: parsePsimi25Interaction function now supports more than one 'entry' items in one 'entrySet' node
New functions: replace methods for interactors, , taxId, organismName and releaseDate added (all for psimi25InteractionEntry objects)
New functions: replace methods for interactors, , taxId, organismName and releaseDate added (all for psimi25InteractionEntry objects)
Biostrings
Added a consmat method for AlignedXStringSet objects.
KEGGgraph
version 1.1.5: dependence on Rgraphviz is set to 1.22.0
MCRestimate
We are now dependend on Biobase 2.5.5 as this is required by golubEsets 1.4.6
GenomeGraphs
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/GenomeGraphs] permanent link
aroma.light
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowViz
Changed email address in all of my packages
flowCore
some changes in the filter definition that were needed for flowClust integration
aroma.light
removed quotes from do.call
flowCore
making sure the data is copied when generating a workflow
bioDist
candidate 'list' methods (KLD) for comparing samples of unequal size
affy
Rolled back r37752. Fixed affydata instead.
Fixed a cel file read issue related to the affydata package.
KEGGSOAP
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
beadarray
- fixed bug in createBeadSummaryData(). rownames are now assigned to se.exprs and NoBeads slots.
- fixed bug in plotBeadIntensities(). Changed variable name of intensities from 'I' to 'intens' and now checks that there are 1 or more items for plotting.
- fixed bug in plotBeadDensities() - when 'col' and 'arrays' was specified, lines weren't coloured correctly.
- new arguments tiffExtGrn and tiffExtRed in readIllumina() allowing user to specify tiff extensions. Previously assumed all tiffs ended in _Grn.tif or _Red.tif, however this is not always the case.
- updated readIllumina() and createBeadSummaryData() documentation
flowCore
adding a coersion method to manyFilterResult
mdqc
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowCore
Cleaned up some of my comments.
Perry's updates to the introduction and conclusions.
affy
Small change to bg.correct.mas to allow chips that have some probesets missing MM probes to be processed. Note that this will still result in NA expression values for these probesets.
affy
Removed usage (or reference) to pstricks tex style in BioC vignettes.
flowViz
plotting arguments are now passed on to the time line plots
MCRestimate
hello
big update many new features, individual votes for example
bug removed
affycoretools
Added AnnotationDbi to Imports
[/affycoretools] permanent link
BAC
added the BAC package
flowCore
Bumped version no
Updated biexponential transform so that it now calculates
the solution of a generic biexponential function
S(x,a,b,c,d,f) = ae^(bx) -ce^(-dx) +f instead of the logicle function
it was calculating earlier.
Updated Logicle transformation: The implementation of the logicle
transform
was found to be different from that described by Parks et al. A new C
function
was implemented for the logicle transformation reflecting the method
described
in the paper. Additionally, the parameter argument f passed to the
logicle
function was missing a multiplying factor a.
fixing the subsetting of views
We want to be able to add numerics or characters to a workflow
adding support for subsetting operations in workFlows
plw
Temporarily removed the part of HowToPLW that uses limma (limma does not load)
DFP
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
simpleaffy
forgot to bump version number
fixed minor documentation issues
ArrayTools
Added affydata to the Suggests field and added the complete list of dependencies.
ArrayExpress
Does not replace 0 by NA anymore
?\195?\130add the phenoData
[/ArrayExpress] permanent link
GEOquery
2.5.3
-----
Thanks to Jonathan Dreyfuss for suggesting a change to deal with 'null' in GSEMatrix files
* Added na.strings=c('NA','null','NULL') to the parseGSEMatrix read.delim() call
2.5.2
-----
* Changed GDS2MA and GDS2eSet to have the default behavior of fetching the Annotation GPL file for inclusion in the eSet or MAList
2.5.1
====
* Added ability to download Annotation GPL files that often include more information than standard GPL files because they are curated by GEO against the Entrez Gene database
affycoretools
Removed support for soon to be defunct class exprSet.
[/affycoretools] permanent link
GEOquery
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
ArrayExpress
Divided the main function ArrayExpress into two functions:
- getAE to download and unzip the archive from the database.
- magetab2bioc to convert mage tab files into bioconductor object even
if the files are stored locally.
- The function AEproc2bioc, by Juok Cho, is made to deal with processed data.
[/ArrayExpress] permanent link
bioDist
Updated the equation for KLDist.matrix method to incorporate division
by number of bins.
Modified the KLdist.matrix method for signature "list"
affyio
(1.7.8) Minor changes to the pgf/clf parsing code. In particular functionality for assessing whether the required fields in the headers are present.
MVCClass
Removed usage (or reference) to pstricks tex style in BioC vignettes.
GenomeGraphs
Forgot to add the Overlay.R file :)
[/GenomeGraphs] permanent link
flowCore
add elements in the papaer, especially in the Results and Discussion section
affy
Fixed creation of .affyInternalEnv to ignore the functions designed to allow updating the AffyBatch methods. Previously we ended up with 'yBatch.methods' as one of the normalize.AffyBatch.methods or 'orrect.methods' as one of the pmcorrect.methods.
RankProd
Updated all examples and vignettes to use Dilution dataset, not defunct affybatch.example. Bumped version.
ArrayTools
This adds 6 new packages to the repository and manifest.
The new packages are: MEDME, edgeR, PLPE, logitT, ArrayTools and
microRNA.
affy
Fixes to minimize the size of affy package in BioC 2.3 and BioC 2.4.
GeneRegionScan
Corrected misleading feedback in geneRegionScan() function
[/GeneRegionScan] permanent link
GenomeGraphs
Fixed attribute names to work with Ensembl 50
[/GenomeGraphs] permanent link
ArrayTools
Altered initialize method so that R can call new("designMatrix")
R has changed and now if you want to use initialize you must be
careful that any specified parameters are also defined and defaulted
such that the object can be made by a call to new(). This is
necessary because the object has to be able to be made by new() in
order to be extendable.
pkgDepTools
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
daMA
Changed biocViews entry of Statistics to Bioinformatics.
xps
for testing disable examples in prefilter.Rd and unifilter.Rd
beadarray
fixed the mismatches from documentation object 'readBGX'
fixed the parser warnings and made the man pages more readable
affy
Removed unneeded geneplotter dependency.
flowCore
added vectorized version of figure 1
flowCore
update to close connection on exit
added a isFCSfile function
GeneRegionScan
-updated documentation of addSnpPdata to match previous update
- updated the addSnpPdata function so that it can now take individual names from pData columns. This is useful in sets such as the GSE9372 where all samples are in triplicates. This update also allowed to delete the horrible addHapMapSnpPdata function.
[/GeneRegionScan] permanent link
aroma.light
Version: 1.13.3 [2009-07-15]
o ADDED: fit- and backtransformXYCurve().
o Added attribute 'processingTime' to the fit object returned
by fitPrincipalCurve().
xps
update to version xps-0.99.5
- updated files: Makefile.win, configure.win, xps.Snw, README, ACKNOWLEGMENT
flowCore
making sure all parameters in a flowSet are the same
mdqc
Fixing a link in man page to pam function.
edgeR
Updated DGEList function in classes.R to order data by group
Resolving changes from unique() ---> levels(); topTags.R changed so more robust
affyio
(1.9.1) Fix parsing problem for calvin command console format CEL files on big endian machines.
flowFlowJo
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowCore
added flowQ figure to paper
some updates to the paper
stepNorm
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
flowCore
Fixed man page link issue.
flowCore
some more coercion methods
affycoretools
Converted many of the dependencies from Depends to Imports. This removes the functions in these packages from the search path, which will speed things up.
[/affycoretools] permanent link
rMAT
Added scanDate slot to Biobase's eSet class, added functionality in affy to utilize the new scanDate slot and updated all the packages that create direct subclasses of eSet, ExpressionSet or NChannelSet.
GeneRegionScan
Added scanDate slot to Biobase's eSet class, added functionality in affy to utilize the new scanDate slot and updated all the packages that create direct subclasses of eSet, ExpressionSet or NChannelSet.
[/GeneRegionScan] permanent link
ArrayExpress
Fix the special character from the man page
[/ArrayExpress] permanent link
beadarray
Altered the way spot coordinates are recorded. They are now the floor of the minimum value is now removed, rather than the minimum value itself. This is also recorded in the xOffset and yOffset slots in the BeadLevelList.
flowViz
introduced gpar argument to xyplot in order to pass along graphical parameters to the gate plotting
xps
update to xps-1.5.12
- add method XGeneChipHyb::CheckChipType() to satisfy miRNA-1_0.CDF
- update XGCProcesSet::MaxNumberCells() for miRNA-1_0.CDF
- update XGCProcesSet::DoMultichipExpress() to reduce memory when filling and reading temporary trees
- update XQuantileNormalizer::Calculate() to reimplement trimmed mean
ArrayTools
Updated eSet objects and bumped package version numbers.
convert
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
xps
update to xps-1.5.10
- update XPSPreprocessing.cxx to reduce memory consumption
xps
update to version xps-0.4.0
- import.data: import CEL-files from different directories
- updated DESCRIPTION, NAMESPACE
- added possibility to apply non-sepcific filters and univariate filters
- added S4 classes Filter, PreFilter, UniFilter
- added S4 classes FilterTreeSet and AnalysisTreeSet
pkgDepTools
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowCore
We are able to read files without PnE keyword now. The default of '0,0' is used and a warning is issued
KEGGgraph
format fix: invalid whitespace in item is fixed
xps
update to xps-1.5.14
- update export() to include read.table(..,comment.char='')
- update methods.DataTreeSet.R to allow probe-level lowess and supsmu normalization
- update rwrapper.cxx to allow probe-level lowess and supsmu normalization
- update DoMultichipExpress() to remove problem with step size stepout for more than 10000 trees
- protect XSectorBackground, XWeightedBackground against numCells4Bg=0
- in XPSNormalizer.cxx change targetinten for logbase
- in image.dev and boxplot.dev correct missing mar and las
- make utils namePart, extenPart public and add man
plier
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
KEGGgraph
Version bumped to 0.8.7: pdf vignette added, plotKEGGgraph function with new paramter 'nodeRenderInfo'
plotKEGGgraph adds nodeRenderInfo parameter
RankProd
fixed some minor doc issues
flowViz
updated default graphical parameters system
affy
Small bugfix -- normalize.AffyBatch.invariantset() had a call to chipNames(abatch) that should have been sampleNames(abatch). Thanks to Markus Schmidberger for pointing this out.
KEGGSOAP
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
BAC
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
GeneRegionScan
- improved abstract() of the expressionset output from getLocalMetaprobeIntensities
[/GeneRegionScan] permanent link
beadarray
updated control information to contain HumanV1
xps
update to xps-1.3.13
- update DESCRIPTION to mention root version
- update README
edgeR
made automatic y-axis scale for MA plots
made automatic y-axis scale for MA plots
more modifications to vignette
add plotMA.R
add plotMA.Rd
fixed code/doc inconsistency
fixed dumb error in Sweave vignette file
fixed verbose output, fixed topTags error when n large
added plotMA, added doPoisson argument to deDGE, changes examples in vignette
ArrayExpress
Add man pages for processed data functions
Fix man pages and namespace
[/ArrayExpress] permanent link
affy
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
flowCore
added a more programatic interface to create transformMaps
MCRestimate
debug vignette
edgeR
Files and documentation for two new functions, splitIntoGroups and splitIntoGroupsPseudo added
flowCore
changed eval methods for polytope and ellipsoid gates
xps
update to version xps-0.5.0
- eliminated memory leaks in C++ code parsing generic CEL-files
- C++ source code can now be compiled with MS Visual C++
beadarray
Updated control info for Humanv1 chip
Removed large data objects and example zip file
Some improvements to documentation
flowCore
adding functions to write flowFrames and flowSets to FCS files
pkgDepTools
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
flowCore
Fixed issue with the wrong min range when reading in a fcs file , bumped version no
making sure the range parameter is ignored for clipping after the data has been transformed
affycoretools
One more fix to account for changes to biomaRt.
[/affycoretools] permanent link
iterativeBMA
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/iterativeBMA] permanent link
bioDist
Removed usage (or reference) to pstricks tex style in BioC vignettes.
plier
make it compile on openSUSE 11.0/gcc 4.3.1
BAC
added the BAC package
flowViz
changing some default colors for things
xps
update to xps-1.1.4
- update vignette xps.Snw
- add new vignette APTvsXPS.Snw
- update examples script4exon.R
- add examples script4xps2apt.R and script4bestmatch.R
- update README
webbioc
Fixing webbioc to work with ExpressionSet objects
affycoretools
Bugfixes for changes in bioma
Modified biomaRt-specific functions to account for the fact that the MySQL interface has been removed from that package.
Made change to reflect removal of Dilution from the affy package. The data resides in affydata.
[/affycoretools] permanent link
ArrayExpress
expression values of processed ExpressionSet are numeric
[/ArrayExpress] permanent link
aroma.light
Version: 1.11.1 [2009-01-12]
o Added fit- & backtransformPrincipalCurve().
Version: 1.11.0 [2008-10-21]
o The version number was bumped for the Bioconductor devel version.
Version: 1.10.0 [2008-10-21]
o The version number was bumped for the Bioconductor release version.
affycoretools
Fixed two bugs in probes2tableBM
[/affycoretools] permanent link
affyio
(1.7.4) Fix issue related to parsing CDF file probeset units which do not have MM probes when using the binary xda format. This refers to an issue described/illustrated in this mailing list message: https://stat.ethz.ch/pipermail/bioc-devel/2007-October/001403.html
fix for decode_UINT8_t which was incorrectly returning an uint16. This should not have any effect for users using AGCC/Generic Binary Format CEL files, but improves the general robustness of the core parsing code.
plw
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affy
Updating the license reference to reflect R standards.
GeneRegionScan
Changed version number to indicate that it is ready for publishing
[/GeneRegionScan] permanent link
mdqc
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
xps
update Makefile.win for root_v5.22.00
stepNorm
Use generic residuals functions to extract residuals in calcAIC and calcBIC.
Fixed residual extraction in calcAIC and calcBIC when the residuals are passed in directly.
xps
update to xps-1.1.5
- correct problem in validData for CEL-files starting with numbers
qvalue
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
edgeR
This update introduces two new functions, equaliseLibSizes and estimateCommonDisp, to edgeR. equaliseLibSizes takes a DGEList object and a fixed value for phi and adjusts the count data so that library sizes are approximately equal. It contains code from quantileAdjust, but no iterative procedures. If the argument phi is set to 0, then the Poisson model is used to equalise the libraries. Allowing for phi to be an argument required some modifications to be made to interpolateHelper. estimateCommonDisp takes fixed count data, assuming library sizes are equal (i.e. pseudodata generated by equaliseLibSizes), and estimates the common dispersion parameter. This function is based on findMaxD2, with the option for using Newton-Raphson feasible for use here, as estimates from NR method that fall outside the (0,1) domain for delta are corrected using a grid search. This fix should probably be applied to findMaxD2. Documentation for interpolateHelper has been extended, but no documentation files have been provided for the two new functions.
KEGGSOAP
Requst KEGG API v6.2 instead of v6.0.
Fixed a typo in KEGGSOAP.R.
Bumped up version number to 1.19.1.
MCRestimate
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
impute
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
MCRestimate
removed quotes from do.call
GSEAlm
Added the package GSEAlm to Bioconductor.
impute
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affycoretools
Removed hgfocus from Suggests, as it isn't used.
more tweaks to modify the suggests/depends to be on .db annotations
changed the vignette depends entries
[/affycoretools] permanent link
GEOquery
cleaned up and documented some old code. Also, did away with gunzipping and used gzfile directly.
flowCore
more on the outline
more cleaning up of name space
flowCore
fixed hyperlog transforms, compensation and added EH transforms
dealing with conflicts between Florians and Nishants versions
started to clean up the classes
GenomeGraphs
Slight change for clearer documentation on arguments of gdPlot
Bumped version number to 0.99.1 so the package can be included in the upcoming Bioc release
This adds package GenomeGraphs to bioconductor.
[/GenomeGraphs] permanent link
xps
Adding support for Mac OS X build.
edgeR
1 June 2009, edgeR 1.3.3
- paste() replaced with file.path() in vignette.
xps
update to xps-1.3.1
- update XPSSchemes.cxx to handle xxx.annot.na26.cvs correctly
- add function root.merge.data()
factDesign
Use coef function to extract model coefficients rather than relying on list subscripting. This was required due to changes from R 2.6.x to R 2.7.x.
flowViz
Fixed a bug/typo in timeLinePlot function.
factDesign
Changed documentation to reflect that the estrogen data set is an ExpressionSet rather than an exprSet object.
prada
adding functionality to specify xrange as a function
flowCore
fixed bug in coercion to flowFrame for empty frames
added import for plot generic
prada
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
beadarray
- fixed bug in findAllOutliers() - indexes were incorrect when negative values were present and logs were taken. Thanks to Jonathan Cairns for pointing this out.
- updated the beadarray vignette to include our BMC Research Notes paper.
affyio
(1.7.6) Add C code level pgf file parser. Note that no method of accessing the data stored in a PGF file at the R level has been provided (and may not ever be provided).
Biostrings
unit tests for XString and inheriting classes
xps
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xps
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
topGO
Interim version
flowCore
more updates to the documenation an a number of little buf fixes
flowCore
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowViz
bumped version
make S4 class links Windows-friendly
affycoretools
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/affycoretools] permanent link
AnnBuilder
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
flowViz
fixing a bug in the flowFrame densityplot method
affy
Updated affybatch.example
prada
fixing some grid issues
xps
update to version xps-0.4.2
- add support to import generic (calvin) CEL-files
- update method volcanoplot
flowCore
fixing some issues with manyFilterResults
plw
Added citation
rMAT
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
weaver
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
xps
Added support back for Windows.
flowCore
another for subsetting of empty flowFrames
fixing bug when subsetting empty flowFrames
HELP
Updated dependencies to get rid of warnings.
DFP
Adds the DFP package to the manifest and repos.
xps
update to xps-1.3.3
- change variable path of XFolder to gFolderPath (see TFolder)
- update ExportExprTrees() to allow missing annotation tree
- correct bug in rwrapper.cxx PreprocessRMA() preventing normalize=FALSE
- change intensity<- to allow using slot data for further processing
- add help for intensity<-
GEOquery
fixed parseGSE when GSEMatrix=FALSE to use textConnections again; was failing to adjust for _table_end stuff
Biostrings
latex tag change to get package to build.
Modifications to alignment documentation to begin discussion on new changes to code.
makecdfenv
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowCore
bumping version
fixing some minor issues with keywords
DFP
Updated eSet objects and bumped package version numbers.
flowCore
changed the link fin filter-methods from itself to Subset
RdbiPgSQL
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affy
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GEOquery
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowCore
fixed bug in splitting of flowSets by factors
beadarray
Changed email address for package maintainer
flowViz
fixing documentation
GEOquery
Rebuilt Vignette
factDesign
added NAMESPACE
beadarray
Added HULK normalization method. Normalization based on BASH neighbourhood finding and weighted average of residuals. R & C code added along with Rd files.
flowViz
bumping version number
more documentation updates
beadarray
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
beadarray
Removed unneeded geneplotter dependency.
GenomeGraphs
minor fixes
Added a number of help pages for the new helper functions
[/GenomeGraphs] permanent link
affycoretools
Small fix to hyperGoutput. The output of annotation(GOHyperGResult) no longer contains the .db suffix, so this has to be added back on.
[/affycoretools] permanent link
minet
update 1.1.5
flowCore
fixed a number of bugs in data import and basic plotting functions
edgeR
updated LGPL version
aroma.light
Version: 1.13.1 [2009-05-13]
o Incorporating the same updates as in release v1.12.1.
Version: 1.13.0 [2009-04-20]
o The version number was bumped for the Bioconductor devel version.
Version: 1.12.1 [2009-05-13]
o BUG FIX: backtransformPrincipalCurve(..., dimensions) did not subset
the 'X' matrix. Also, the method now returns a matrix of the same
number of columns requested. The Rd example now illustrates this.
Thanks to Pierre Neuvial, UC Berkeley for the troublshooting and fix.
affyio
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
rMAT
A third configure file change to support GSL.
Another configure file change to support GSL.
Rebumping the version number.
Bumping the version number for the upcoming release.
ChIPpeakAnno
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/ChIPpeakAnno] permanent link
MCRestimate
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
KEGGgraph
Adds KEGGgraph to the repository.
flowViz
lpolygon methods now return the gate outlines and the contour function is fixed
GEOquery
Fixed some problems with vignette and added comments about raw data download
beadarray
Small fix to beadLevelQC, where previously the outlier plot overwrote the background control plot in the HTML output
xps
update to xps-1.5.11
- update DoMultichipExpress() to reduce memory when filling temporary trees
ArrayExpress
Uncomment the example in man.
[/ArrayExpress] permanent link
xps
Adding support for xps on wilson1.
xps
update to version xps-0.3.12
- updated XGeneChip::ReadData() to allow parsing of AffyProbeMiner CDFs
- updated S4 class ProjectInfo and file NAMESPACE
- added class XProjectHandler as base class for XDataManager, XProcessManager
- updated import.data.R and rwrapper.cxx
- updated files SchemeTest3.root and DataTest3_cel.root
xps
Unsupported on wilson1 too (64-bit openSUSE 11.0). A bug in the gcc version shipped with this OS makes it too complicated to install ROOT on wilson1. Not worth the trouble sorry. Hopefully openSUSE 11.1 (to be released in December) won't have this problem.
unsupported on Windows (no ROOT)
flowViz
improvements to the timeLine plots
using a better metric to detect temporal anomalies now in timeLinePlot
flowCore
changes suggested by Ryan and Josef
flowCore
some changes of the paper and addition of work flows
bioDist
updated doc for KLdist.matrix
Fixed KLdist.matrix method for signature matrix
KEGGSOAP
fixed a typo
flowCore
we are a bit more relaxed about this 10 bit bug in BC FCS files now. When we see the CPX keyword we warn that we fixed the file, if it's not there we still proceed (with 16 bit) but give a more urgent warning
MCRestimate
updated documentation
added NAMESPACES
flowCore
more verbose error messages when getting out of index on a filter
affy
Tightened up package imports.
impute
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
affycoretools
Updated BiocViews.
[/affycoretools] permanent link
flowCore
more updates to the documenation an a number of little buf fixes
many little fixes of the documentation
mdqc
Moved cluster and MASS from Suggests field to the Depends.
GEOquery
2.5.3
-----
Thanks to Jonathan Dreyfuss for suggesting a change to deal with 'null' in GSEMatrix files
* Added na.strings=c('NA','null','NULL') to the parseGSEMatrix read.delim() call
stepNorm
Fixed residual extraction in calcAIC and calcBIC when the residuals are passed in directly.
GenomeGraphs
Forgot to add the Overlay.R file :)
According to a number of patches from Elizabeth Purdom (many thanks!) The following changes have been made:
*.) drawOverlay : changed added to Overlay.R -- modified code to be TextOverlay, RectangleOverlay. Additional refactoring should occur where we remove arguments/member-variables from TextOverlay which are irrelevant. Added helper functions of the form:
to <- makeTextOverlay(text = "Some Text!", xpos = .5, ypos = .5, coords = "absolute")
*.) Added the TextOverlay class.
*.) Added fill, and color arguments to the RectangleOverlay to support the coloring of the rectangle lines and the innards separately.
*.) Added showDisplayOptions, which either takes an object, or a character string and prints out the DisplayPars that the object expects.
*.) Added method drawGD for Segmentation class
*.) .drawSegments now can do vectorized coloring and different lwd for elements of the Segmentation list.
*.) Added convenience function segmentation to construct segmentation objects more readily -- this tries to make that clunky list format less of a pain.
*.) Made a number of tweaks for better displaying the legend. Added convenience function for making legends
*.) fixed a display bug in Transcript
*.) added labelRot, labelColor, and labelCex for the gdPlot function.
[/GenomeGraphs] permanent link
GEOquery
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
fixed getAndParseGSEMatrices to use gzfile--thanks to Martin Morgan for doing the homework and suggesting a fix for using gunzip (which does not work on Windows).
added citation
flowViz
fixing timeLine bug
flowCore
bumping version
'readFlowSet' was overly verbose
allowing to use transformList objects in transform calls
simpleaffy
Replaced reference to soon to be defunct class exprSet with ExpressionSet.
plw
Bumped Z
prada
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowCore
moved all plotting stuff to flowViz, flowCore now issues a message to attach flowViz for all plotting
makecdfenv
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
beadarray
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
flowViz
making sure we get a reasonable variance estimate in the timeLinePlots
fixed bug in desnityplot
KEGGSOAP
moved XML, SSOAP and RCurl off of the search path
xps
Adding build support on Windows.
Added specification of cl and link executables based on MSVSPATH environment variable.
update config.win
update to version xps-0.99.4
- updated files: config.win, findvc.pl
Added support for builds on wellington.
Adding support for Mac OS X build.
GEOquery
Changed references from exprSet to ExpressionSet in the documentation to reflected changes that were made in the code.
prada
Small change to vignette to get package to build.
beadarray
createBeadSummaryData.c - binarySearch function correction
rMAT
I have added a check in the MATScore function so that if cName is not contained in the control it will stop.
RdbiPgSQL
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
maigesPack
Changing maintainer email adress
GSEAlm
Added pooled-variance option to lmPerGene; minor bib and style updates.
xps
update to version xps-0.4.3
- new method rawCELName() to get the names of the imported CEL-files
- update XGeneChip::ImportTransAnnotation() to import alignment with best score
maigesPack
Changed biocViews entry of Statistics to Bioinformatics.
qvalue
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
affy
Remove code trying to create MIAME and phenoData using tkWidgets
- The underlying code (in Biobase and more extensively in tkWidgets)
is broken and not easily fixed; widgets can still be used to select
files.
Documentation tidy (removing empty sections and corrected usage)
SIM
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
fixing up an isue that arose due to others putting name spaces in place
xps
update to version xps-0.3.11
- corrected export.Rd
- added method MAD() to TStat.h
affy
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowViz
cleaned up code for gate plotting and added documentation
affycoretools
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/affycoretools] permanent link
iterativeBMA
This adds pkg iterativeBMA to the bioc 2.3 repos.
[/iterativeBMA] permanent link
flowCore
updated docs for transformations
edgeR
updated LGPL version
GenomeGraphs
Added NEWS file as well as added a small plotting type change to BaseTrack.
[/GenomeGraphs] permanent link
flowCore
fixed some minor bugs in the ncdf stuff and bumped version number
introducing netcdf storage for flowFrames
undo mechanism for workFlows and error handling
ArrayExpress
queryAE input more complete, http instead of ftp, HTTPUserAgent with name of the package for tracking pruposes
[/ArrayExpress] permanent link
xps
update to xps-1.5.3
- correct memory leak in function XGCProcesSet::DoMultichipExpress()
- update exonLevel.Rd
flowViz
converter from norm2Filter to ellipse
affyio
(1.7.17) Minor fixes for CLF/PGF parsers
bioDist
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
genomeIntervals
Bumping the version number for the upcoming release.
[/genomeIntervals] permanent link
affy
explictly export methods on previously defined functions, so other
packages can importMethodsFrom(affy, ...)
Rtreemix
adapted to the new version of the package graph and updated documentation
ArrayExpress
fix a small problem in extract.zip
Should work even on file names not starting by E-, need to test after Mohammad changes
Use of unzip instead of int.unzip
[/ArrayExpress] permanent link
minet
Adds minet to the 2.3 repos and the manifest.
ArrayExpress
Change save settings, FALSE by default
[/ArrayExpress] permanent link
flowCore
fixed warnings for missing documenation during R CMD check
KEGGgraph
KEGGgraph 0.8.16: in case SPIA package is not available the backup data will be loaded in the vignette from KEGGgraph package. This is only for the beta-phase
flowCore
initialisation method for flowFrame
simpleaffy
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
webbioc
fixed Rd issues found by Rdversion 2 parser
KEGGgraph
KEGGgraph Update Version 1.1.1: improved render of KEGG pathway graphs with new interface of Rgraphviz
affy
I added exportClasses("AffyBatch") to the NAMESPACE.
I also tried to disambiguate a name collision in expresso, where 'normalize' and 'bg.correct' were used as function
arguments (logical vectors) and were also used to refer to functions of that same name.
GenomeGraphs
Update to work with biomaRt >= 1.99.0
[/GenomeGraphs] permanent link
xps
update to xps-1.5.2
- correct memory leak in function XWeightedBackground::Calculate()
- change vignette extension to .Rnw
beadarray
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Small edit to ExpressionControlData manual page
Added missing alias for backgroundCorrect-RGlist to manual pages
Updated data object containing definitions of control probes for expression platforms.
GenomeGraphs
Some reasonably large changes which will probably mess up R CMD CHECK, but need to get these in here at some point. They include a new object which should replace the various forms of annotation plotting.
[/GenomeGraphs] permanent link
KEGGgraph
update to 0.8.14
Explains how to retrieve KGML files remotely
Get rid of underscores to avoid Windows version crash
adding KGML files for merging
Introducing how to retrieve KGML file remotely
KEGGgraph
neighborhood returns unique restuls
Upgrade to 0.8.9
Add neighborhood method: to extract neighborhood set of given node(s)
edgeR
Poor man's quantile adjustment functions.
flowViz
more vignette and documentation improvements
updates of the vignette
edgeR
another change to the way 'show' displays objects
flowViz
densityplot updates for multiple channels
topGO
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
xps
update to xps-1.1.8
- correct bug in class XINICall resulting in buffer overflow
xps
update to version xps-0.99.10
- update source code to handle tmpdir correctly on WinXP
- update examples script4xps.R and script4exon.R
- update README
affy
Patch for the bug on se.exprs when subsetting an AffyBatch
(reported by Nicolas Delhomme).
The actual fix differs from Nicolas' patch in the sense that
no new method 'intensity.sd' is added (affy should probably
be on maintenance mode until something unified comes up).
GEOquery
Added RUnit as a "suggests:" to fix warning
beadarray
bug fix to manual page of ExpressionControlData.Rd
xps
update to version xps-0.99.8
- update functions root.xxx to work with WinXP
- update Makefile clean
- update examples/script4xps.R
iterativeBMA
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/iterativeBMA] permanent link
GenomeGraphs
Small bugfix for the retention of dimensions on the intensity matrix, thanks to Elizabeth Purdom.
[/GenomeGraphs] permanent link
GEOquery
2.3.3
=====
* GSM and GDS parsing speedup of 20 to 50 FOLD
KEGGgraph
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
KEGGgraph
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowCore
update to documentation and addition of methods
factDesign
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
DFP
Changed biocViews entry of Statistics to Bioinformatics.
flowCore
some updates of the paper manuscript
xps
update to xps-1.5.1
- update validData() to check for duplicate rownames
- update XGeneChip::ImportProbeInfo() to allow both headers of xxx_probe.tab
- update XGeneChipHyb::ReadGenericDataHeader() for genetitan plate data
simpleaffy
Changed biocViews entry of Statistics to Bioinformatics.
aroma.light
Version: 1.9.2 [2008-09-11]
o Added argument 'onMissing' to normalizeFragmentLength() for specifying
how to normalize (if at all) data points for which the fragment lengths
are unknown. For backward compatibility, we start of by having it
"ignore" by default.
o MEMORY OPTIMIZATION: robustSmoothSpline() is now cleaning out
more variables when no longer needed.
Version: 1.9.1 [2008-05-10]
o Incorporating the same updates as in release v1.8.1.
Version: 1.9.0 [2008-04-29]
o The version number was bumped for the Bioconductor devel version.
Version: 1.8.1 [2008-05-10]
o BUG FIX: If the 'subsetToFit' of normalizeFragmentLength() was
shorter than the number of data points, an exception was thrown.
The test was supposed to assert that the subset was not greater
than the number of data points.
flowCore
minor fixes: typo and biblio
beadarray
=- change to readIllumina to allow new bead-level data to be read in (when textType=_perBeadFile.txt)
impute
Removed whitespaces from Rd files containing /items{stuff} {
xps
for testing change Makefile.win and add Makefile.winMT
update to xps-1.3.8
- update all initialize methods to prevent checkS3forClass warnings
- update bgcorrect.rma, bgcorrect.mas5
- update script4xps.R, script4exon.R
- update manual file bgcorrect.Rd
flowCore
using alias tables for the workflow identifiers now
xps
update to xps-1.5.5
- eliminate memory leaks caused by branch addresses
- update root.expr.R, root.call.R and rwrapper.cxx to open root file only once
GOSemSim
Adds GOSemSim to the repository.
RdbiPgSQL
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowCore
fixed bugs in filtering methods related to droppig of dimensions
affyio
(1.7.9) add functions to CLF parsing code for converting from/to probe_id and (x,y) pairs
widgetInvoke
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/widgetInvoke] permanent link
ChIPpeakAnno
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/ChIPpeakAnno] permanent link
flowCore
some changes in the filter definition that were needed for flowClust integration
updated definition and constructor for ellipsoidGates to contain stupid distance parameter
aroma.light
Version: 1.7.1 [2007-11-28]
o The startup message when loading the package is generated with
packageStartupMessage() so that it can be suppressed.
o Package now only suggest the R.oo package, and instead depends
on the new R.methodsS3.
o TYPO: Corrected a spelling error in the help pages.
o Package passes R CMD check R v2.6.1.
Version: 1.7.0 [2007-10-08]
o The version number was bumped for the Bioconductor devel version.
Version: 1.6.0 [2007-10-08]
o The version number was bumped for the Bioconductor release version.
annotationTools
corrected bug in getHOMOLOG.R
[/annotationTools] permanent link
affyio
(1.9.1) Fix parsing problem for calvin command console format CEL files on big endian machines.
maigesPack
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
AnnBuilder
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
edgeR
fixed a few examples that were affected by the unique() ---> levels() change
Changed unique() to levels() in a bunch of cases
rMAT
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Fixed a small bug when calculating MATScores
Fixed a small bug when calculating MATScores
Rtreemix
modifed man files
Rtreemix
make it compile on openSUSE 11.0/gcc 4.3.1
affy
Updating the NEWS file on the new scanDates slot in eSet.
Added scanDate slot to Biobase's eSet class, added functionality in affy to utilize the new scanDate slot and updated all the packages that create direct subclasses of eSet, ExpressionSet or NChannelSet.
RankProd
fixed Rd issues found by Rdversion 2 parser
fixed Rd issues found by Rdversion parser
GEOquery
fixed for check
GEOquery
2.3.2
=====
* Hopefully fixed GSEMatrix parsing on Windows. Thanks to Henrik Bengtsson and Uwe Ligges for pointers. The issue was download.file using text mode, which on Windows for .gz files causes problems.
* GSEMatrix parsing is now the default for getGEO when downloading GSE records. This ends up being many orders of magnitude faster for most GSE records.
affycoretools
Small bug in vennSelectFC that resulted in incorrectly named fold change columns in the output.
[/affycoretools] permanent link
flowCore
some more coercion methods
weaver
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
annotationTools
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/annotationTools] permanent link
flowFlowJo
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
GenomeGraphs
fix in man page to remove warning of CMD check
[/GenomeGraphs] permanent link
BAC
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
plier
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowCore
removed quotes from do.call
mdqc
Added the new mdqc package to the repository.
edgeR
Deleted equaliseLibSizes and estimateCommonDisp as they are not documented
Deleted files without documentation - equaliseLibSizes, estimateCommonDisp, q2qnbinom, qnbinom qpoispm
annotationTools
eliminated email address from DESCRIPTION file
added coment.char='#' to Affymetrix annotation file commands in the vignette
[/annotationTools] permanent link
flowCore
update to documentation and addition of methods
iterativeBMA
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/iterativeBMA] permanent link
flowCore
Fixing an issue with the parameters slot
xps
update to xps-1.5.9
- update XQuantileNormalizer to reduce memory and increase speed
- update validOption() to allow 'separate:none'
flowViz
fixed bug in densityplot when data in flowFrame is empty
AnnBuilder
Changes to enable AnnBuilder to work with GO.db instead of GO.
GO is going away, so these changes are needed to depend on GO.db
instead. To complete the transformation with a minimal rewriting of
AnnbBuilder, it was also necessary to include some functions from
AnnotationDbi so that the GO environment GOTERMS could be made into a
alive just a little bit longer for those times when someone comes
looking for annotation packages for "platypus", or any other unusual
types of model organisms.
flowCore
edits to the vignette
GSEAlm
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
MCRestimate
RF bug fixed
fix bug in table if factor is in incorrect order
MantelCorr
Changed biocViews entry of Statistics to Bioinformatics.
affyio
(1.7.13) read.celfile() now includes a additional argument allowing the user to specify reading only the intensity values from the specified CEL file (ie exclude STDEV and NPIXEL)
xps
update to xps-1.3.10
- for testing update Makefile.win for root debug version
- update DESCRIPTION
ArrayTools
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
plier
Updated reference to the return object to reflect it is of class ExpressionSet rather than exprSet.
maigesPack
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
edgeR
fixed rounding issue (thanks tom hardcastle)
GSEAlm
minor
minor
minor
minor
minor
GSEAlm: minor tweaks for upcoming release
xps
unsupported on Windows (no ROOT)
xps
update to xps-1.5.8
- for root_v5.24.00 C++ functions returning TString must return TString(0) instead of 0
- update XQuantileNormalizer to allow improved ties handling as option like preprocessCore
- update rma() and rwrapper.cxx to allow ties handling and to open root file only once
flowCore
fixing bug when coercing flowSet to flowFrame
ArrayExpress
Clearer error messages
[/ArrayExpress] permanent link
flowCore
fixed default for curv1Filters gridsize
doc fixes
maigesPack
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowCore
A first draft of the new workflow infrastructure and all the little changes that were necessary to make that work. This might eventually move to some other place. Also updated the documentation a bit. More to come soon...
updated show method to deal with new transform parameter slot
beadarray
Fixed bug where all bead-level plots were saved as jpeg ,despite setting fileType argument
affy
(1.17.12) bg.correct.rma now calls the appropriate code from preprocessCore.
Removed the c source code files (rma_background2.c, rma_background2.h).
Removed bg.correct.rma2()
(1.17.10) rma() now uses rma background correction routines from preprocessCore, rather than the previously used internal affy hybrid R/c code implementation
flowCore
changes to the manuscript based on suggestions by Robert
ArrayExpress
Handling of multiple array design
[/ArrayExpress] permanent link
KEGGgraph
version bumping to 0.8.13. The last update before the next release
add translateKEGGgraph and its helper functions
update plotKEGGgraph function to be able to plot translated pathway graphs
version bumping
getDisaplyName does not stop if the display name cannot be found, it just fill the not-found names with the raw node name
version bumping
queryKEGGsubgraph uses subKEGGgraph function instead of subgraph function to subset the node/edge information too
updated vignette, spelling fixes
version bumping
updated vignette
obsolete help files
add function 'queryKEGGsubgraph' to query subgraph of a KEGG graph with given genes as nodes
annotation functions moved annotation.R
edgeR
Changed biocViews entry of Statistics to Bioinformatics.
initial changes to vignette
rMAT
Readme
Change for windows
Change Makevars.win
topGO
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
GEOquery
Removed usage (or reference) to pstricks tex style in BioC vignettes.
genomeIntervals
check_valid removed from interval_union code (was not documented)
[/genomeIntervals] permanent link
GSEAlm
GSEAlm 0.99.1: trimmed dependencies to bare minimum
MVCClass
Replaced reference to soon to be defunct class exprSet with ExpressionSet.
bridge
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
maigesPack
Cleaned up setMethod("[", ... definitions to work with R 2.8.x.
GenomeGraphs
Temporary fix for biotype problem
[/GenomeGraphs] permanent link
HELP
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowCore
Changes for Gating ML 1.5 compliance
MCRestimate
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
affy
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
SIM
changed maintainer to Maarten van Iterson
xps
update to xps-1.5.13
- update export(), attachExpr(), attachCall(), attachPVal() to avoid too many open files
- update mas5(), xxx.call() and rwrapper.cxx to open root file only once
- update XPSBase, XPSData, XPSPreprocessing, rwrapper to allow setting bufsize for tree baskets
- update express() to allow setting bufsize for tree baskets
flowCore
modify NAMESPACE
affycoretools
Added AnnotationDbi to imports section in NAMESPACE file.
[/affycoretools] permanent link
GenomeGraphs
Added Rd files for makeTranscript, makeGene and makeGeneRegion
[/GenomeGraphs] permanent link
prada
adding functionality to specify xrange as a function
flowViz
fixing bug in timeLinePlot
ABarray
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
flowCore
fixed bug when reading flowSets from an annotated data frame specifying FSC files that are spread across several directories
SIM
added citation
GOSemSim
bug fixed for calling *switch* function. use "=" not "<-" within the *switch* function.
ArrayExpress
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
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KEGGgraph
Bumping the version number for the upcoming release.
GSEAlm
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GenomeGraphs
A small change to the NAMESPACE, and a fix to some of the Annotation stuff
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HELP
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affyio
(1.7.12) Fixes for C level command console format CEL file parsing. In particular the functions generic_get_detailed_header_info() and gzgeneric_get_detailed_header_info() had problems in some situations where various algorithm parameters were not stored as character strings.
xps
update to xps-1.3.7
- update Makefile.win
- update script4xps.R and script4exon.R
- update manual files prefilter.Rd and unifilter.Rd
xps
Bumped pkg versions for BioC 2.5 devel line.
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flowCore
adapting file IO to work on artifactual values
edgeR
cast the data into matrix class (to avoid some weirdness on data frames)
geneRecommender
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GEOquery
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.
affyio
(1.7.16) Fix bpmap problems on big endian machines (eg ppc, sparc). This is the same problem that affected and was fixed for little endian machines a number of months ago. To the user it manifested itself with the error message "Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'", but in fact caused by incorrect parsing of the bpmap file version number.
Rtreemix
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affycoretools
Added imports(AnnotationDbi, get) so things like get(goid, GOTERM) will work.
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KEGGgraph
Bumped pkg versions for BioC 2.5 devel line.
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ABarray
Bumped pkg versions for BioC 2.5 devel line.
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impute
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowViz
fixed bug in plotting of ellipse gates
flowCore
fixed transformList constructor
edgeR
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowCore
fixed inconsitencies in the splitting methods
xps
update to version xps-0.99.7
- try to remove warning for Mac build
ArrayExpress
A new package by Audrey Kauffmann to access the ArrayExpress Repository
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flowCore
some cosmetic code rearrangements
flowViz
added lines and polygon methods (glines, gpolygon for now) that allow for adding of gates to existing plots
affyio
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
MCRestimate
debug some things, vignette
affy
Apparent keyboard short-cut accident in earlier commit.
Unexplainable FORTRAN error here, preventing me from going
through the complete R CMD check.
Fixed propagation of changes in subsetting.
bridge
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowCore
same fix for unionFilters
fixing intersectionFilter
affycoretools
Added AnnotationDbi to the Depends field.
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rMAT
Added package rMAT to svn
ArrayTools
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
iterativeBMA
Updated eSet objects and bumped version number.
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edgeR
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
ArrayExpress
add the QT_list.txt file in inst/doc
Major changes that allow the package to cover most of the database
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edgeR
Moving comment lines around.
geneRecommender
Replace usage of soon to be defunct class exprSet with ExpressionSet.
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ArrayExpress
add argument extract to getAE and extract_path to extract.zip
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flowFlowJo
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flowCore
fixing documentation
update for revised version of the manuscript: logicle reference, flowCore vignette...
KEGGSOAP
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ArrayExpress
- Corrected the attachment of the phenoData to the object when multiple
ADF files
- The XML package is now in Imports not in Depends
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annotationTools
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
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edgeR
Bumping version numbers for BioC 2.4 devel.
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fixed global variable warning
fixed bug when maximizing weighted likelihood
edgeR
add R files
fixed problem in examples, added 4 text files (eventually for vignette)
Rtreemix
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GeneRegionScan
-corrected missing shQuote around the metaProbeSetsFile variable in getLocalMetaprobeIntensities
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xps
update to xps-1.3.12
- correct bug in TUnivariateTest::FDR and Hochberg
- add method TUnivariateTest::BY
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impute
Changed biocViews entry of Statistics to Bioinformatics.
rhdf5
Moving rhdf5 back to Rpacks.
annotationTools
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flowViz
adding alias to man pages
flowCore
added workFlow to vignette
edgeR
Common dispersion on phi and delta scales added to output for alpha.approxeb
genomeIntervals
a warning at building is removed by importing intervals v.0.12.2 and importing class "Intervals_virtual_or_numeric"
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KEGGgraph
updated the note of retrieveKGML file for windows users. Thank the report and discussion from Takeshi Nishiyama, National Insitute of Public Health in Japan
affyio
(1.7.16) Fix bpmap problems on big endian machines (eg ppc, sparc). This is the same problem that affected and was fixed for little endian machines a number of months ago. To the user it manifested itself with the error message "Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'", but in fact caused by incorrect parsing of the bpmap file version number.
bridge
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
edgeR
small modifications to 'exactTestNB' defaults
ArrayExpress
Fix the problem with the path in getAE and extract.zip
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daMA
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
affyio
(1.11.1) Fix issue with stack exhaustion in pthreads builds with read.probematrix()
makecdfenv
Removed usage (or reference) to pstricks tex style in BioC vignettes.
edgeR
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
flowCore
added some accessors for common operations
bioDist
trying to fix up the man page here
plier
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
GEOquery
Fixed getDirListing to close a temporary textConnection
GeneRegionScan
Fixed a man page issue involving a list of DNAString objects.
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ArrayExpress
Bumped pkg versions for BioC 2.5 devel line.
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affy
(1.19.4) The method by which rma/justRMA access the median polish code from preprocess core has been changed. There should be no user noticable impact.
KEGGgraph
XML news did not specify the change of xmlChildren exactly, therefore a relative new version (2.3) is used.
debug of parseKGML: change of XML package (xmlChildren returns list() instead of NULL in case of no children) raised issue solved. Thanks the report and fix of Matt Settles (Washington State University), and the report of Yongjin Li. Working version 1.1.2
AnnBuilder
Standardizing reference to Artistic License 2.0.
affyio
fix for decode_UINT8_t which was incorrectly returning an uint16. This should not have any effect for users using AGCC/Generic Binary Format CEL files, but improves the general robustness of the core parsing code.
flowFlowJo
Added package flowFlowJo to the repository
flowViz
added lines method for ellipsoidGates
HELP
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
flowCore
many little fixes
fixed little spelling bug in read.FCS
Rtreemix
Bumping version numbers for BioC 2.4 devel.
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plw
Fixed problem with bg.correct.rma2
flowCore
corrected teh addSignifCurv argument to addSignifCurvRegion
fixed Rd parser warnings
xps
update to xps-1.3.2
- update XPSBase.cxx NewFile() to handle tmp files for certain dirnames correctly
affyio
(1.11.1) Fix issue with stack exhaustion in pthreads builds with read.probematrix()
GEOquery
Removed the constantly-out-of-date count of samples in GEO from the vignette
GenomeGraphs
Commiting a small number of changes: made the drawGD method public, allowed for the biomart member variable of a GeneRegion to be NULL - this change is to allow for the introduction of a annotationSource object.
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affycoretools
Last of the changes to biomaRt-specific functions, due to the removal of MySQL interface from biomaRt.
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GSEAlm
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
GEOquery
Fixed (using a bit of a hack) the problem of reading
an entire table, including the !sample_table_end
when the IDs are numeric.
GeneRegionScan
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
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Biostrings
Improved vwhichPDict() speed by using vmembers() internally for
adding the ids of the duplicated patterns to the result.
Added a full example showing how to use it to map probe set IDs
between chips.
Bumped version to 2.13.2.
xps
update to version xps-0.3.12
- updated XGeneChip::ReadData() to allow parsing of AffyProbeMiner CDFs
- updated S4 class ProjectInfo and file NAMESPACE
- added class XProjectHandler as base class for XDataManager, XProcessManager
- updated import.data.R and rwrapper.cxx
- updated files SchemeTest3.root and DataTest3_cel.root
flowCore
I start to add text to the introduction and different section.
affyio
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
xps
update to xps-1.1.9
- protect class XRMABackground against defect Affy chips, e.g. zero division
- protect root.data() etc against duplicate celnames or treenames
daMA
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowCore
fixed issue in automated detection of time channel
beadarray
Fixed bug where the array QC failed on some arrays with sections missing or having no outliers in the negative controls
Documented missing arguments in some manual pages
rMAT
Windows Error - the comments doesn't work
Windows Error - comments mman.h
Linux Error - add library in the header
Validity check option
Validity check option
flowViz
introducing netcdf storage for flowFrames
xps
update to xps-1.1.6
- prevent import of CEL-files with zero max intensity
- update functions returning ExprTreeSet to import results as option only
- update functions returning CallTreeSet to import results as option only
- update root.density etc to allow saving from R function
- add root.profile to use root graphics for boxplots
- add summarization method FARMS (Hochreiter et al)
- add summarization method DFW (Chen et al)
- update vignette xps.Snw
GSEAlm
minor
GEOquery
Adding more tests
flowCore
Changes Nolwenn suggested
MCRestimate
fixed some code and docu in order to bring the package back onto bioconductor
GenomeGraphs
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
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beadarray
Bug fix to manual page of ExpressionControlData.Rd
affycoretools
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
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affyio
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
webbioc
Bumped pkg versions for BioC 2.5 devel line.
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minet
update 1.6.0
update
flowViz
improved plotting of gates
ArrayExpress
Made shorter examples to improve time of the check
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qvalue
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
flowCore
updated Documentation
GOSemSim
bug fix
GenomeGraphs
Some minore changes that probably break things.
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factDesign
Removed usage (or reference) to pstricks tex style in BioC vignettes.
xps
update to version xps-1.1.1
- increase maximum root file size from 2GB to 2TB
- decrease computation time
- correct bug preventing export of exon probeset normalized data
flowViz
fixed namespace
ArrayExpress
Corrections to man pages
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prada
Removed unneeded geneplotter dependency.
Removed unneeded geneplotter dependency.
makecdfenv
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
beadarray
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
ArrayExpress
Add functions getcolproc and procset to handle processed data. Only works on simple cases so far.
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Biostrings
Minor change to provide quality methods to objects in ShortRead package.
Enhancements to pairwise alignment suite.
* Improved the mismatchTable and mismatchSummary to generate more information for AlignedXStringSet and PairwiseAlignment objects.
* Created a QualityAlignedXStringSet class to make it easier to determine if quality scores were used in the alignments.
* Added a quality function for extracting the quality measures from QualityAlignedXStringSet objects.
* Code and documentation housekeeping to make it easier to maintain.
Made the pairwiseAlignment function arguments more generic.
daMA
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
MantelCorr
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
makecdfenv
Use the recently added Rzlib library in R-devel on Windows.
prada
added alias to documentation to get rid of warning message during R CMD checK
Rtreemix
fixed Rd issues found by Rdversion 2 parser
maigesPack
updated serialized graph objects
prada
removed quotes from do.call
flowCore
work on the new layout
affycoretools
Removed hgfocus from Suggests, as it isn't used.
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annotationTools
1) In examples given in .Rd files: to accomodate for the change in Affymetrix file format, added "comment.char='#'" when reading-in Affymetrix annotation files
2) removed email address in .Rd files
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affy
Use the recently added Rzlib library in R-devel on Windows.
beadarray
oops - typo in the function name
better to use the name space and import just what we need
added a missing dependency
an Rd file in the R directory
flowCore
fixed bug in boundaryFilter and added some more detailed documentation
changed the link fin filter-methods from itself to Subset
xps
update to version xps-0.3.10
- added chipname to function import.expr.scheme
- added further annotation items to export
edgeR
Biobase package in Imports: instead of Depends: field.
topGO
Fixes a problem caused by changes in the structure of the underlying annotations.
The annotations changed to depend on org packages for all relevant
data. Thus, the join that is required to get data from a probe
package involves one more step. This change just modifies this join
so that things will work.
affyio
(1.7.9) add functions to CLF parsing code for converting from/to probe_id and (x,y) pairs
Rtreemix
added the Rtreemix package and removed the bim package
flowCore
ncdf is no longer a strict dependency
flowViz
making sure the truncated sample names are still unique
aroma.light
Version: 1.13.1 [2009-05-13]
o Incorporating the same updates as in release v1.12.1.
Version: 1.13.0 [2009-04-20]
o The version number was bumped for the Bioconductor devel version.
Version: 1.12.1 [2009-05-13]
o BUG FIX: backtransformPrincipalCurve(..., dimensions) did not subset
the 'X' matrix. Also, the method now returns a matrix of the same
number of columns requested. The Rd example now illustrates this.
Thanks to Pierre Neuvial, UC Berkeley for the troublshooting and fix.
ArrayExpress
Always numerics values, and function getcolraw to extract possible column names and avoid downloading twice when setting rawcol is needed.
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SIM
url added to DESCRIPTION file
Rtreemix
docs update
xps
update to xps-1.3.9
- add function MetaProbesets to xps.def
- update rwrapper.cxx
bioDist
Changed biocViews entry of Statistics to Bioinformatics.
flowViz
updated DESCRIPTION
bugfix: honor xlim and ylim in 1-D plot()
affycoretools
updated an example, as affybatch.example is now gone
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geneRecommender
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MantelCorr
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plw
Increased z
KEGGgraph
queryKEGGgraph uses addNode from graph package, which was not specified before. It could have led to bug in case the graph library is loaded before the KEGGgraph. The bug is solved in the version 1.1.10 by David
annotationTools
updated CITATION file
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weaver
Update maintainer email address for pkgDepTools and weaver
qvalue
House Cleaning: Removing INDEX files from svn. These files are created in the build process and shouldn't be version controlled.
ArrayTools
Patched because the anotation packages changed names.
ArrayExpress
Minor changes to code mostly on cleaning up after usage. Used some patches from Andrew Tikhonov.
[/ArrayExpress] permanent link
Biostrings
Add vcountPattern, to count occurrend of pattern in XStringSet-derived
objects
Pushed PairwiseAlignment S4 object creation to C level in preparation for a time when the output is vectorized to a greater extent.
Fixed a bug when aligning an empty string.
simpleaffy
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Rtreemix
\name{confIntGPS-methods}
\docType{methods}
\alias{confIntGPS}
\alias{confIntGPS-methods}
\alias{confIntGPS,RtreemixData,numeric-method}
\title{Method for calculating GPS values and their 95\% bootstrap
confidence intervals}
\description{
The method first calculates the genetic progression score (GPS) for the
patterns in a given dataset \code{data} based on a fitted mutagenetic trees
mixture model with \code{K} components. The \code{data} and \code{K}
have to be specified. Then, it derives a 95\% confidence intervals for
the GPS values with bootstrap analysis.
}
\usage{
\S4method{confIntGPS}{RtreemixData,numeric}(data, K, ...)
}
\arguments{
\item{data}{An \code{RtreemixData} object containing the samples
(patterns of genetic events) for which the GPS values and their
bootstrap confidence intervals are to be calculated. The number
of genetic events should NOT be greater than 20.}
\item{K}{An \code{integer} larger than 0 specifying the number of
branchings in the mixture model.}
\item{...}{
\code{sampling.mode} is a \code{character} that specifies the
sampling mode ("constant" or "exponential") used in the waiting time
simulations. Its default value is "exponential".
\code{sampling.param} is a \code{numeric} that specifies the
sampling parameter corresponding to the sampling mode given by
\code{sampling.mode}. Its default value is 1.
\code{no.sim} is an \code{integer} larger than 0 giving the number of
iterations for the waiting time simulation. Its default values is
10000.
\code{B} is an \code{integer} larger than 0 specifying the number of
bootstrap samples used in the bootstrap analysis. Its default value
is 1000.
\code{equal.star} is a \code{logical} specifying whether to use
equal edge weights in the noise component. The default value is
\code{TRUE}.
}
}
\value{
The function returns an object from the \code{RtreemixGPS} class that
containes the calculated GPS values, their 95\% confidence intervals,
the model used for the computation, the data, and so on (see
\code{\link{RtreemixGPS-class}}). The GPS values are represented as a
\code{numeric} vector with length equal to the number of samples in
\code{data}. Their corresponding confidence intervals are given in a
matrix with two columns.
}
\note{
The data for which the GPS values and their corresponding
confidence intervals are to be calculated should not have more
than 20 genetic events. The reason for this is that the number of all possible patterns
for which the GPS values are calculated during a computationally intensive simulations
is in this case 2^20. This demands too much memory.
The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
For trying out the code please copy it and uncomment it.
}
\author{Jasmina Bogojeska }
\seealso{
\code{\link{RtreemixGPS-class}}, \code{\link{gps-methods}},
\code{\link{RtreemixData-class}}, \code{\link{RtreemixModel-class}},
\code{\link{fit-methods}}
}
\examples{
}
\keyword{methods}
\name{gps-methods}
\docType{methods}
\alias{gps}
\alias{gps-methods}
\alias{gps,RtreemixModel,RtreemixData-method}
\alias{gps,RtreemixModel,matrix-method}
\alias{gps,RtreemixModel,missing-method}
\title{Methods for predicting the GPS of given dataset by
using a given mutagenetic trees mixture model}
\description{
These functions compute the genetic progression score (GPS) of each
sample in the given \code{data} by performing a waiting time
simulation along the branchings of the mixture model \code{model}. The
model has to be specified. If a dataset is missing a GPS for all
possible patterns is calculated. The number of events of the samples
in \code{data} equals the number of genetic events in the \code{model}.
}
\usage{
\S4method{gps}{RtreemixModel,RtreemixData}(model, data, ...)
\S4method{gps}{RtreemixModel,matrix}(model, data, ...)
\S4method{gps}{RtreemixModel,missing}(model, data, ...)
}
\section{Methods}{\describe{
\item{model = "RtreemixModel", data = "RtreemixData", ...}{A method for calculating
the GPS values of the data given as \code{RtreemixData} object.}
\item{model = "RtreemixModel", data = "matrix", ...}{A method for calculating
the GPS values of the data given as 0-1 \code{matrix}.}
\item{model = "RtreemixModel", data = "missing", ...}{A method for calculating
the GPS values of the set of all possible patterns.}
}}
\arguments{
\item{model}{An object of the class \code{RtreemixModel} specifying
the mutagenetic trees mixture model used for deriving the GPS values.
The model should NOT have more than 20 genetic events.}
\item{data}{An \code{RtreemixData} object or a 0-1 \code{matrix}
containing the samples (patterns of genetic events) for which the GPS values
are to be calculated. The length of each of them has to be equal
to the number of genetic events in the \code{model}.}
\item{...}{
\code{sampling.mode} is a \code{character} that specifies the
sampling mode ("constant" or "exponential") used in the waiting time
simulations. Its default value is "exponential".
\code{sampling.param} is a \code{numeric} that specifies the
sampling parameter corresponding to the sampling mode given by
\code{sampling.mode}. Its default value is 1.
\code{no.sim} is an \code{integer} larger than 0 giving the number of
iterations for the waiting time simulations. Its default value is 10.
\code{seed} is a positive \code{integer} specifying the random generator
seed. Its default value is (-1) and then the time is used as a
random generator.
}
}
\value{
The function returns an object from the \code{RtreemixGPS} class that
containes the calculated GPS values, the model used for the
computation, the data, and so on (see
\code{\link{RtreemixGPS-class}}). The GPS values are represented as a
\code{numeric} vector with length equal to the number of samples in \code{data}.
}
\references{Estimating cancer survival and clinical outcome based on
genetic tumor progression scores, J. Rahnenf\"urer et al. }
\note{
The mixture model used for deriving the GPS values should not have more than
20 genetic events. The reason for this is that the number of all possible patterns
for which the GPS values are calculated during a computationally intensive simulations
is in this case 2^20.
The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
For trying out the code please copy it and uncomment it.
}
\author{Jasmina Bogojeska}
\seealso{
\code{\link{RtreemixGPS-class}}, \code{\link{RtreemixData-class}},
\code{\link{RtreemixModel-class}},
\code{\link{fit-methods}}, \code{\link{confIntGPS-methods}}
}
\examples{
}
\keyword{methods}
\keyword{survival}
%\VignetteIndexEntry{Rtreemix}
%\VignetteDepends{methods, graph, Biobase, Hmisc, Rgraphviz}
%\VignetteKeywords{Rtreemix, mtreemix, disease progression, HIV}
%\VignettePackage{Rtreemix}
%\documentclass[a4paper, oneside, 10pt]{article}
\documentclass[a4paper,12pt,twoside]{article}
\usepackage[pdftex]{graphicx}
\usepackage{calc}
\usepackage{sectsty}
\usepackage{caption}
\renewcommand{\captionfont}{\it\sffamily}
\renewcommand{\captionlabelfont}{\bf\sffamily}
\allsectionsfont{\sffamily}
% page style %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[a4paper, left=23mm, right=23mm, top=20mm, bottom=20mm, nohead]{geometry}
\setlength{\parskip}{1.5ex}
\setlength{\parindent}{0cm}
\pagestyle{empty}
\usepackage{Sweave}
\SweaveOpts{prefix.string = Rtreemix}
\title{\vspace*{-6ex} {\bf Rtreemix}: a package for estimating mutagenetic trees mixture models and genetic progression scores}
\author{Jasmina Bogojeska, J\"org Rahnenf\"uhrer}
\date{\today \\%
\texttt{http://www.mpi-sb.mpg.de/$\sim$jasmina}}
\begin{document}
\maketitle
<
options(width = 70)
@
\section{Introduction}
The mixture of mutagenetic trees introduced in \cite{Beer12005} is an
evolutionary model that provides an interpretable probabilistic
framework for modeling multiple paths of ordered accumulation of permanent genetic changes that
can be used for describing many disease processes. Each path captures a possible route of
disease development. These models are used to model \texttt{HIV} progression characterized
by accumulation of resistance mutations in the viral genome under drug pressure \cite{Beer12005} and
cancer progression by accumulation of chromosomal aberrations in
tumor cells \cite{Rahn2005}. From the mixture model, a genetic progression score (\texttt{GPS})
can be computed for each patient \cite{Rahn2005} that gives an estimate of the
disease progression and can be used for specifying therapies or estimating survival times of the patients.
Both the mixture model itself and the derived \texttt{GPS} values are shown to improve the
interpretation of disease progression and to have predictive power for estimating the drug resistance
in \texttt{HIV} \cite{Beer12005} or the survival time in cancer \cite{Rahn2005}.
Beerenwinkel \textit{et al.} in \cite{Beer22005} introduced the \texttt{Mtreemix} package implemented in
\texttt{C/C++} that provides an efficient code for estimating the mutagenetic trees mixture models from cross-sectional
data and using them for various predictions. Building up on the \texttt{Mtreemix} software and using the \texttt{C/C++} API that
\texttt{R} provides, we created the \texttt{Rtreemix} package. By reusing already existing \texttt{C} functions
our package provides the users with \texttt{R} functions as efficient as the
programs available in the \texttt{Mtreemix}.
Similar to \texttt{Mtreemix}, the \texttt{Rtreemix} package provides functions
for learning the mixture model from given data, simulation, likelihood computation
and estimation of the GPS values. Furthermore, it introduces new functionality for estimating genetic
progression scores with corresponding bootstrap confidence intervals and for performing stability
analysis of the mixture models \cite{Bogo2008}.
\section{Structure and Functionality}
The class structure of the \texttt{Rtreemix} package is given in Figure~\ref{fig:classes}.
\begin{figure}[!h]
\centering
\includegraphics[width=0.7\linewidth]{ClassDiagram.pdf}
\caption{Class diagram of the package \texttt{Rtreemix}. The diagram illustrates the classes with their attributes and the relationships among them.}
\label{fig:classes}
\end{figure}
In this way, all data structures and information connected to some entity, like the mixture model or the data for the model estimation,
are packed together, which makes the code compact and easy to understand and work with. In what follows we will present
a working scenario in which we will use and briefly discuss most of the functions available in \texttt{Rtreemix}. More detailed information
about the parameters of all the functions used in the text bellow and their default values can be found in the help files of the package.
First, we load the package.
<
library(Rtreemix)
@
\subsection{The Dataset and the \textit{RtreemixData} class}
The datasets used for estimating the mixture models consist of binary patterns that describe the occurrence
of a set of genetic events in a set of patients. Each pattern corresponds to a single patient. The set of genetic
events comprises genetic changes relevant for the disease taken into consideration. In \texttt{Rtreemix} the data used for
estimating a mutagenetic trees mixture model is represented as an object of the class \texttt{RtreemixData}.
We consider the dataset from the Stanford \texttt{HIV} Drug Resistance Database \cite{Rhee2003} that comprises genetic
measurements of 364 \texttt{HIV} patients treated only with the drug \textit{zidovudine}. This dataset is given as an \texttt{RtreemixData} object
\textit{hiv.data.RData} in the \textit{data} folder of the package and can be loaded and displayed as follows.
<
data(hiv.data)
show(hiv.data) ## show the RtreemixData object
@
It should be also pointed out that a text file with a specific format can be used for creating an object of class \texttt{RtreemixData}. An example of
such file is the file \textit{treemix.pat} in the \textit{examples} directory of the package. The text files used to create an \texttt{RtreemixData}
object should follow the format of this file. Using \textit{treemix.pat} the \texttt{RtreemixData} object is created as follows.
<
ex.data <- new("RtreemixData", File = paste(.path.package(package = "Rtreemix"), "/examples/treemix.pat", sep = ""))
show(ex.data) ## show the RtreemixData object
@
One can also create an \texttt{RtreemixData} object by specifying the set of patient profiles as a binary matrix as shown in the code below.
<
bin.mat <- cbind(c(1, 0, 0, 1, 1), c(0, 1, 0, 0, 1), c(1, 1, 0, 1, 0))
toy.data <- new("RtreemixData", Sample = bin.mat)
show(toy.data)
@
Additionally, there are functions for listing the set of profiles, the genetic events, the patient IDs, the number of events and the number of patients in the dataset.
<
Sample(hiv.data)
Events(hiv.data)
Patients(hiv.data)
eventsNum(hiv.data)
sampleSize(hiv.data)
@
\subsection{Learning mutagenetic trees mixture models}
Having a set of patterns that indicate the occurence of genetic events for a group of patients
we can learn a mutagenetic trees mixture model. The model is an object of the \texttt{RtreemixModel} class that extends the
\texttt{RtreemixData} class. We fit a 2-trees mixture model for the \texttt{HIV} data \cite{Rhee2003}.
<
mod <- fit(data = hiv.data, K = 2, equal.edgeweights = TRUE, noise = TRUE)
show(mod)
@
The tree components of the fitted model can be visualized as follows.
\setkeys{Gin}{width=.9\linewidth}
\begin{figure}[!t]
\centering
<
plot(mod, fontSize = 15)
@
\caption{The mutagenetic trees mixture model for the \texttt{HIV} dataset.}
\label{fig:hiv}
\end{figure}
When the mixture model contains a large number of tree components it is convenient to be able to plot a specific tree component. The following code plots the
second tree component of the mixture model learned from the \texttt{HIV} dataset.
<
dev.off()
plot(mod, k=2, fontSize = 14)
@
It is assumed that mixture models with at least two components always have the noise (star) component as a first component. When only one tree component is fitted to the given data it can be either a star or a nontrivial tree component based on the choice of the parameter \texttt{noise}.
The mixture components comprising the model are represented as a list of directed \texttt{graphNEL} objects, and their weights (the mixture parameters) are given as a numeric vector. There are functions for getting the mixture parameters of the model, the number of tree components, the dataset used for estimating the model, etc.
<
Weights(mod)
Trees(mod)
getTree(object = mod, k = 2) ## Get a specific tree component k
edgeData(getTree(object = mod, k = 2), attr = "weight") ## Conditional probabilities assigned to edges of the 2nd tree component
numTrees(mod)
getData(mod)
@
This class can also contain other useful information connected with the mixture model: an indicator for the presence of the star component, a matrix of the responsibilities of each tree component for each pattern of the data used for learning the model, a matrix of the complete dataset in case of missing data, etc.
<
Star(mod)
Resp(mod)
CompleteMat(mod)
@
The mutagenetic trees mixture model encodes a probability distribution on the set of all possible patterns \cite{Beer12005}.
<
distr <- distribution(model = mod)
distr$probability
@
One can also generate a random mutagenetic mixture model. In this case each tree component from the model is drawn uniformly at random from the tree topology space by using the Pr\"ufer encoding of trees. The number of tree components and the number of genetic events have to be specified. Additionally, one can specify the range from which the edge weights of the tree components are randomly drawn ($[0.2, 0.8]$ in the example bellow).
<
show(rand.mod)
@
It is also possible to fit a mixture model and analyze its variance by deriving confidence intervals for the mixture parameters and the edge weights
(resulting from a bootstrap analysis). An example for this is given in the PDF file \textit{ExtendedVignette} in the \textit{doc} folder of the package.
\subsection{The \texttt{likelihood} method}
The package \texttt{Rtreemix} implements the function \texttt{likelihoods} which calculates the (log, weighted) likelihoods for
the patterns in a given dataset (\texttt{RtreemixData} object) derived with respect to a given \texttt{RtreemixModel}.
The likelihoods are contained in an object of class \texttt{RtreemixStats} which extends the \texttt{RtreemixData} class.
The number of the genetic events in the patterns from the given dataset has to be equal to the number of genetic events in
the branchings from the given mixture model. In the code that follows we calculate the likelihoods of the \texttt{HIV} dataset
with respect to the fitted mixture model.
<
mod.stat <- likelihoods(model = mod, data = hiv.data)
Model(mod.stat)
getData(mod.stat)
LogLikelihoods(mod.stat)
WLikelihoods(mod.stat)
@
When having the weighted likelihoods, one can easily derive the responsibilities of the model components for generating the patterns
in the specified dataset.
<
getResp(mod.stat)
@
\subsection{The \texttt{sim} method}
The mutagenetic trees mixture model encodes a probability distribution on the set of all possible patterns for a specified set of genetic events.
The \texttt{sim} method provides the possibility of simulating (drawing) patterns from a given \texttt{RtreemixModel}. The simulated patterns
are then returned as an \texttt{RtreemixData} object. Let's draw a specified number of patterns from our randomly generated model.
<
data <- sim(model = rand.mod, no.draws = 300)
show(data)
@
When besides the mixture model also the sampling mode and its respective sampling parameter are specified, this function simulates
patterns together with their waiting and sampling times from the respective model. The waiting and sampling times result from a waiting
time simulation along the branchings of the mixture model. The \texttt{sim} method presents the results in an \texttt{RtreemixSim} object.
An example illustrating this is given in the PDF file \textit{ExtendedVignette}.
\subsection{The genetic progression score (\texttt{GPS})}
When assuming independent Poisson processes for the occurrence of events on the edges of each mixture component
and for the sampling time of the disease, waiting times can be mapped on the tree edges of the branchings.
Consequently, a genetic progression score (\texttt{GPS}) that incorporates correlations among events and time intervals among
occurrences of events can be associated to the mixture model as proposed in \cite{Rahn2005}. The \texttt{GPS} estimates the
stage of the disease and is important for estimating survival times and giving patients proper therapies.
In the \texttt{Rtreemix} package the method \texttt{gps} calculates the \texttt{GPS} of a given set of patterns
with respect to a specified mixture model (an \texttt{RtreemixModel} object). The GPS values are derived in a waiting time
simulation for a given large number of simulation iterations, and for a specified sampling mode ("constant" or "exponential")
and its corresponding sampling parameter. The result of the \texttt{GPS} calculation is given as an
object of the class \texttt{RtreemixGPS} which extends the class \texttt{RtreemixData}. Moreover, with the function \texttt{confIntGPS}
the package gives the possibility to analyze the variance of the \texttt{GPS} values.
This function first calculates the \texttt{GPS} for the patterns in a given dataset data based on a fitted \texttt{K}-mutagenetic trees
mixture model. Then, it derives a 95\% confidence intervals for the \texttt{GPS} values with
bootstrap analysis. The data and \texttt{K} have to be specified. The confidence intervals reflect the variability of the
estimated \texttt{GPS} values. The results are again given as an \texttt{RtreemixGPS} object. The usage of the functions \texttt{gps}
and \texttt{confIntGPS} is demonstrated in the PDF file \textit{ExtendedVignette}.
\section{Stability analysis with the \texttt{Rtreemix} package}
The \texttt{Rtreemix} package implements functions that can be used for assessing the quality and analyzing the stability of different attributes of the
mutagenetic trees mixture model (the probability distributions induced by the model, the number of tree components, the
topologies of the tree components, the GPS values and so on). This is usually done by first choosing a model attribute of
interest and its appropriate similarity measure, and then inspecting its stability in a simulation setting.
In the simulation study typically attributes from simulated true mixture models are compared with the corresponding attributes from
models fitted to observations drawn from these true models. The similarity between the true and the fitted model is then
compared to the similarities between the true and a sufficient number of random models sampled uniformly from the mixture model space.
The quality of a fitted attribute is then assessed by estimating a p-value as the percentage of cases in which the true model is closer
to a random model than to the fitted model with respect to the chosen model attribute. More details about performing stability analysis
of the mutagenetic tree mixture modes and interpreting the results can be found in \cite(Bogo2008). Simple code examples for the
stability analysis of a mutagenetic trees mixture models are given in the \textit{doc} folder of the package in the PDF file \textit{ExtendedVignette}.
\bibliography{Rtreemix}
\bibliographystyle{unsrt}
\end{document}
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