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Bioconductor Changlog.
Tue, 13 Oct 2009
SNPchip
Removed usage (or reference) to pstricks tex style in BioC vignettes.
SNPchip
updated annotation files -- build hg18. changed plotCytoband function.
SNPchip
added RatioSnpSet class and basic accessors. Fixed bug in plotting of genotype colors for plotSnp methods
fixed bug in recyclying of plotting symbols and colors
SNPchip
modified help files for chromosome2integer, integer2chromosome
SNPchip
updated vignette
SNPchip
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
SNPchip
added option to graph a plot title in .plotChromosome (see op$main)
SNPchip
bumped version number
add documentation for ratio, classes
SNPchip
updated man pages to fix missing links on the windows platform check -- HmmPredict and RatioSnpSet classes
SNPchip
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
SNPchip
updated licence in the description and a few help files
SNPchip
moved chromosome and position methods to the oligoClasses package
changed Depends to higher version of oligoClasses. UPdated vignette
SNPchip
the show method no longer returns the recycled vector of plotting symbols...this leads to problems when plotting multiple chromosomes
SNPchip
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
SNPchip
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
SNPchip
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
SNPchip
corrected mistake in DESCRIPTION
SNPchip
updated snp-methods
SNPchip
synchronize HmmPredict and SnpLevelSet instances in plotSnp method. Add accessors/documentation.
SNPchip
changed description
added abline option for plotting
SNPchip
several changes to how featureData is accessed for affy platforms
SNPchip
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
SNPchip
slight change to oligoHowTo vignette
SNPchip
added CITATION
SNPchip
added zzz.R file
SNPchip
fix bug in .plot when genotype calls are not available
SNPchip
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
SNPchip
synchronize HmmPredict and SnpLevelSet instances in plotSnp method. Add accessors/documentation.
SNPchip
updates to labeling of y-axes. Put copy number in sample.snpset object on original scale. oligoHowTo shows how to compute copy number from SnpCallSetPlus object
SNPchip
fixed bug in height.predict for plotSnp
added plotting methods when HmmPredict object is provided (package now suggests VanillaICE). plotSnp returns the graphical parameters as a few are updated or modified when plotSnp is called.
SNPchip
removed quotes from do.call
SNPchip
Changed biocViews DNACopyNumber to CopyNumberVariants and SNPsAndGeneticVariability to SNP, GeneticVariability.
SNPchip
Added links to plot method for SnpLevelSet objects to the plotSnp man page to remove minor WARNING from R CMD check.
SNPchip
update man pages. use print instead of show in vignette
SNPchip
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.
SNPchip
changed the getPar method. Added chromosome2numeric function