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Bioconductor Changlog.
Thu, 07 Feb 2008
siggenes
Updated 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
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.
Ringo
added a function to compute overlap between genomic regions in one set with those from another set
Ratlpow
various
annotate
Swapped usage of old style deprecated annotation paradigm with new AnnotationDbi paradigm.
exonmap
updated version number
fixed typo in xmapBridge man page that referred to xmapGene
GOstats
Swapped usage of old style deprecated annotation paradigm with new AnnotationDbi paradigm.
stam
adapted various issues due to new versions of R and Bioconductor
M R/06_predict.R
M R/05_fit.R
M R/04_cv.R
M DESCRIPTION
M data/golubTrain.cv.rda
M data/golubTrain.fit.rda
M man/golubTrain.cv.Rd
M man/plot.stamFit.Rd
M man/golubTrain.fit.Rd
M man/stamPrediction-class.Rd
M man/plot.stamPrediction.Rd
M man/image.stamPrediction.Rd
M man/plot.stamCV.Rd
M inst/doc/tr_2004_03.pdf
SLGI
add function (shareIntMat) to search for pleiotropic gene
Biobase
several doc modifications were made
more cleaning out of exprSet stuff
updating man pages and removing references to exprSet
oligo
Fixed problem with readSummaries identifying the wrong number of samples
Added helper function to read summaries produced by crlmm