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Bioconductor Changlog.
Tue, 13 Oct 2009
Category
Org packages can now be used to make ChrMapHyperGParams
Category
Version Bump.
Fixed bug preventing Ecoli from working with Gostats
E coli has only one (circular) chromosome. So this patch removes the
need for their to be a CHR mapping in the package we are using.
Category
Added a vignette for chromosome band related tools
Category
used makeChrBandInciMat directly instead of MAPAmat since we already have the chr band graph
Category
Was too creative with examples.
Inadvertantly, require()d some packages in a manual page that may not
necessarily be present for everyone. They are still instructive
though, so I placed the offending uses into a dontrun{} block to avoid
headaches for the users of R CMD build.
Category
added a t() that was missing
Category
Updates to fix the vignette issue and warnings with R CMD check
Updated the threshold to select the ribosome pathway
Category
I fixed and documented the behaviour of cateGOryMatrix in cases where 'categ' contains GO categories unknown to the GO package.
The error in R CMD check:
Error in v1[sapply(v1, function(z) !any(is.na(z)))] :
invalid subscript type 'list'
Calls: MAPAmat -> makeChrBandInciMat
was already there and it would be nice if its author could fix it.
Category
fixed a bug reported by Paul Evans, where a zero-length list of categories
induced a whole bunch more zero length vectors and caused no end of problems
with computation of the odds ratio etc
Category
Can't forget to bump that version number...
Category
Removed unecessary class-bloat.
Category
Changed biocViews entry of Statistics to Bioinformatics.
Category
Updated how DatPkgFactory() determines pkg type.
Changed the way the DatPkgFactory() determines package type so that it
should be more robust for the future.
Fixed minor bug that affecting packages with "ag" in the name.
This clears up a bug that would cause packages with "ag" in their
names to become labeled as arabidopsis packages. It also corrects
some mispellings of arabidopis and drops outmoded methods which
existed only to support the defunct LLMappings packages.
Category
Replace the usage of now defunct phenoData class with AnnotatedDataFrame.
Category
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Category
Updating the license reference to reflect R standards.
Category
Modified documentation and error messages.
Trying to make this package and the GOstats package that depends on it
a little friendlier for users.
Category
a first stab at documentation
checked in code for 'linear model' enrichemnt test, currently for chr bands only
Category
Fix to try and clear up ".db" name inconsistencies.
This adds some code to take the name that users put for the
"annotation" of a param and then parse that so that it always removes
the ".db" extension (if they had bothered to type it). This
simplifies the internal representation and allows us to not have to
clear up confusion for users about whether they need to type
hgu95av2.db or hgu95av2 when using the parameter objects since either
will now work the same. Finally, the shorter name is the true prefix
for the package since that is what is used internally to name all the
mappings. Leaving the ".db" around just creates more work for
everyone to clean up via string substitution. Of course if the world
suddenly breaks tomorrow then we will have to reconsider...
Category
Corrects a warning, which was ultimately caused by a typo.
The type was propagated through the code and did not impact the code
itself, but when the .Rd parser was improved, it meant that there were
now codoc mismatches between the manual pages and the strangly spelled
class slots.
Category
bugfix to handle NA p-values
Category
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
Category
importing 'geneIds', 'geneIds<-' and 'ontology' from GSEABase now. Method definitions had to be changed slightly in order to match the new signature.
Category
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Category
Revised imports to be more targeted for the methods and AnnotationDbi packages.
Bumping the version number.
Category
Replaced tab with spaces.
cleanup package dependencies
Category
Updated some man page references to now extinct pkgs.
Fixes a bug when interacting with the org.Sc.sgd pkg.
The org.Sc.sgd.db package is necessarily a strange beast. It is an
organism package, (not a chip based package) but it is also based on
the sgd ORFs instead of probes. So its not a typical org package OR
a typical yeast chip package. This patch adresses this problem so
that this package should hopefulyl work better with GOstats etc.
Category
updating to see if I can get the new yeast packages to work with Category and GOstats
Category
Fixed bug preventing Ecoli from working with Gostats
E coli has only one (circular) chromosome. So this patch removes the
need for their to be a CHR mapping in the package we are using.
Category
bugfix, formatting
Category
bugfix, and bumped version
update to include effect sizes in linear model test output
Category
a patch to get the Arabadopsis code to work - may need more
correction to deal with the multiple gene issue
Category
Fixed breakage introduced by DB schema changes in AnnotationDbi (we recently moved from using old 0.9 schemas to new 1.0 schemas). The package still doesn't pass R CMD check for me but at least GOstats does now (not sure the remaining problems are related to the DB schema changes). Version bump anyway.
Category
Can't forget to bump that version number...
Fix that affects a corner case for KEGGHyperGParams
This fixes a bug that would prevent hyperGTest() from performing as
expected when the annotation package is a chip package.
Category
Fixes bug in getKeggToEntrezMap()
Fixes a bug that was causing getKeggToEntrezMap to grab the wrong data
when an org.Sc.sgd.db package was used.
Category
fixed up the KEGG part so it now works with the org.XX.eg.db packages
Category
updated version
Category
minor change to get this pushed
minor change to the vignette
Category
added doc pages to pass check