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Bioconductor Changlog.
Tue, 11 Mar 2008
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
annaffy
Small bugfix to aafGO(). The id slot of the resulting aafGO objects was incorrectly being set to the probeset ID rather than the GO ID.
flowCore
adding documentation for density filters
snapCGH
altered DNAcopy code to reflect changes in that package
hypergraph
Fixed a matrix subscripting bug and an unlist related warning.
be more careful with parameter names
BCRANK
Added the new package BCRANK to the repository.
cellHTS2
Better colors
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.
ArrayExpress
Add the phenoData to Affy objects created with ArrayExpress and add the save argument to the ArrayExpress2 function
[/ArrayExpress] permanent link
oneChannelGUI
Removing a bug related to limma topTable generation with annotation using yeast2 arrays
[/oneChannelGUI] permanent link
SNPchip
slight change to oligoHowTo vignette
VanillaICE
allow option to plot vertical dashed lines for breakpoints. Updated the fit example data
arrayQualityMetrics
- Modify the boxplot.stats function so that it only detect as outlier the value larger than the others
- Move the on.exit at the right place of the code for AffyBatch
- Correct the logtransform function
[/arrayQualityMetrics] permanent link
Biobase
checkClass unit test