October 2006 affycoretools Added vennSelectFC() which emulates vennSelect() for those cases where there is no replication affyPLM Added preprocess() which does normalization and background correction only affyQCReport Added affyQAReport(), which will create a pdf containing various QA plots for an AffyBatch AnnBuilder Exported resolveMaps() from namespace per user's request Fixed bug in YEASTGENENAME that was not correctly reporting the name annotate Added filterGOByOntology() helper function that takes a vector of GO IDs and returns a logical vector indicating which are in the specified ontology (MF, BP, CC) Biobase Deprecated exprSet and phenoData classes. Methods with exprSet and phenoData in their signature have been deprecated Updated biocReposList to Bioc 2.0 repositories Added lcsuff() to compute the longest common suffix of a set of character strings - this will help to shorten the names of some things like microarray names Added code to make a package from an ExpressionSet biomaRt Fixed exportFASTA() so it works with the data.frame output of getSequence() Enabled use of archived BioMart databases in MySQL mode Fixed a bug in simple biomaRt functions when used on a local BioMart database BSgenome Added the [[ method for BSgenome objects Added the 'length' method for BSgenome objects BufferedMatrix Made as.BufferedMatrix() do more at the C code level to speed things up Added colRanges, colMedians Added filenames(), memory.usage(), disk.usage() methods Category Added DatPkg class to provide abstract interface to annotation data Use filterGOByOntology() for hyperGTest() - this avoids the use of the GOTERM env and should be faster and use less memory Added methods to use humanLLMapping as annotation package Fixed bug in expected count for hyperGTest() cellHTS Changed the output of imageScreen(obj) to integer. Added vertical lines to the boxplot and controls plot to separate different batches flowcore New Package: Provides S4 data structures flow cytometry data. Maintainer: Nolwenn Le Meur genefilter Fixed bug in pAUC computation Fixed bug in rowpAUCs and added class and methods to deal with ROC objects. Added generic and methods for rowFtests GOstats Added helpers for GOHyperGResult objects; sigCategories() - list GO IDs that are significant, selectedGenes() - list genes from selected gene list for given GO ID, plotTermGraphs() - plot connected components of significang GO terms limma read.maimages() with dource = "quantarray" now sets annotation columns Added a namespace to the package. All functions not starting with "." are exported Changed column header for topTable. M renamed logFC, A renamed AveExpr lmFit() not supports ExpressionSet objects, volcanoplot() now allows NULL for names argument New function strsplit2(), which replaces splitName() macat Added warning regarding permutations with small sample sizes makePlatformDesign Fixed bug for NGS parser Fixed problem when generating PDEnvs for NGS Tiling arrays pcaMethods Added parameter 'completeObs' to all pca methods, so end users can choose if the complete observations should be returned Added parameter 'center' to pca methods Changed threshold in ppca() to 1e-5, which will lead to more stable results SNPscan Added a namespace Added accessors for snpcopynumberset Fixed bug in plotSnp Added plotChromosome method plotSnp() is now a wrapper for plotChromosome(). Updated plotCytoband() Renamed SNPscan --> SNPchip ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
[Bioc-devel] NEWS October 2006
1 message · James W. MacDonald