December Changes in BioC Devel

    December 2005

affy
    Fixed a bug in boxplot that prevented main from being set
       
affycoretools
    Added new function hyperG2annaffy to output HTML tables based on the output of hyperGtable
   
altcdfenvs
    Fixed a missing connection argument in the signature for a function (thanks to Norman Pavelka)
    Fix for the parameter 'linebreaks' not being forwarded to subsequent calls

annotate
    Added a new function PMIDAmat
   
arrayQuality
    Added MEEBO array quality plots

beadarray
    New Package:
        Quality control and low-level analysis of BeadArrays
    Maintainer:
        Mark Dunning

bioDist
    Converted functions cor.dist, euc, KLdist.matrix, KLD.matrix, man, MIdist, mutualInfo, spearman.dist and tau.dist to S4 methods
    These functions will dispatch on either matrices or exprSets
   
biomaRt
    Simplified the queryGenerator function
    Fixed useMart function to use 'biomart' argument for non local database
    Fixed bug where gene_stable_id is the filter
    Fixed listMart bug due to non-numeric version index in the msd BioMart
   
Biostrings
    Fixed bug in matchIndexToBioString
    Added a test suite which can be run using testBiostrings()
    Fixed bugs in ShiftOr_matchInternal
    Added a TODO file
    Added bigrandomTGCA.txt (big string of 10 million random TGCA) and a new test in test suite that uses it
    Fixed show method

geneArise
    Implemented dye swap analysis
   
geneplotter
    Added two functions for visualization of distributions
   
GEOquery
    New Package:
        Get data from NCBI Gene Expression Omnibus (GEO)
    Maintainer:
        Sean Davis
GOstats
    Tried to modify GOHyperG to deal with YEAST data
    Added new argument 'universe' to GOHyperG
    Added new function GOKEGGHyperG, an extension of GOHyperG
   
graph
    Add inEdges method to graphAM
    Refactored inEdges documentation
   
iSPlot
    Updated vignette
   
limma
    arrayWeights(method = "reml")now returns correct reml estimates
    arrayWeights now returns a vector of array weights, instead of a matrix
    Bug fix to arrayWeights(method = "genebygene")
    Correct starting information matrix for arrayWeights(method = "genebygene"):, 10(J-1)/J replaced by 10(J-K)/J
   
macat
    Fixed bug in generation of HTML page by plot.MACATevalScoring
    Differential expression scores are now also included in the table of significant probesets
   
made4
    Fixed bug in getdata, nsccia
   
makePlatformDesign
    Added capabilities to read multi-well designs
    Fixed bug in multiPlex
    Fixed bug for NG data
   
MLInterfaces
    Added documentation for xval in clustered computing environments
   
multtest
    Fixed problem with strata (covar) argument in coxY
   
oligo
    Added capabilities to read multi-well designs
    Changed sequenceDesignMatrix to accept general lengths
   
prada
    Fixed bug in popping of viewports
    Fixed bug in plotPlateGrid
    Generalized plotPlate function
    Removed plotPlateGrid
    Interface change to plotPlate
    Fixed bug in imageMap coordinates
    plotPlate now allows for plotting in grid panel layouts
    Added function fpLocate to calculate absolute location of the current viewport
    Added function devRes to get the resolution of the current graphics device
    Fixed bug regarding invalid characters in readFCS
   
RBGL
    Corrected pathname for example in floyd.warshall.al.pairs
    Corrections in is.triangulated man page
    Modified code so triangulation is only tested for undirected graphs
    Added code to test if a set separates two other sets
    maxClique outputs all max cliques
    Deprecated sp.between.old
    New vignette

reposTools
    Deprecated *.packages2 functions
   
Rgraphviz
    Small fixes to prevent a segfault when partial weights are manually declared
   
rhmetis
    Added analysis report for ALL
    Fix passing of edge and node weights
    Change default to use khmetis and SOED
    Cleaned up R interface to hMETIS       
    Added generics for khmetis, hmetis
    Added installation details to README

ScISI
    New Package:
        In Silico Interactome
    Maintainer:
        Tony Chiang


simulatorAPMS
    Updated some man files
   
sscore
    Document changes for easier use of examples

tilingArray
    Replaced seg2confint with confint.segmentation, a wrapper for confint.breakpointsfull from strucchange package
    Removed computeConfInt
    Added class 'segmentation' and methods
    Fixed bugs in plot method for segmentation objects
    The confint method now properly passes arguments level, het.reg, and het.err.
    Fixed bug in documentation for confint.segments
    Fixed documentation for findSegments
    Began converting segmentation result to S4 class
    plotAlongChrom can now also incorporate heatmaps
    Added grid.image
    Improvements on documentation for segmentation class
    Updated vignettes
   
TypeInfo   
    New vignette
    Revision of error messages to be more informative
   
vsn
    Errors due to failures of numerical optimization are now more informative
    Increased efficiency for single stratum analyses
   
xcms
    Replaced clustunique with a C implementation, rectUnique
    Updated to latest version of RAMP
    Added support for reading mzData files
    Now only full-scan spectra are read from mzXML files
    Added checks for blank spectra in RAMP code