February Changes in BioC Devel

    February 2006

affxparser
    Converted publicly available methods from dot-syntax to camel case syntax (e.g., read.cel --> readCel)
    Changes to make the package compile on SUN machines
    It is now possible to specify what readCdfUnits should return
    Addec C functions for fast querying of number of probes in probesets and groupnames in probesets
    Added C function to identify which probes are PM probes
   
affy
    Fixed sampleNames in read.affybatch to conform with row.names of the phenoData slot to match with exprSet validity checking
    Added a new example dataset to allow examples for merge.AffyBatch and ppsetApply to work correctly
    Fixed mva.pairs to accept cex argument for text size of statistics
    Added optional smoothScatter to MAplot, etc
   
affycoretools
    Changed plotDeg and plotHist to automatically extract sample names from the AffyBatch object
    Added filterfun argument to foldFilt to allow for arbitrary filtering of probesets in addition to fold change
    Bugfix in affystart that occured when one has a single chip and uses expression = "mas"
    Bugfix in vennSelect that wasn't ordering HTML tables correctly when number of contrasts == 2
    Moved hyperGtable and hyperG2Affy to GOstats package
   
affyio
    Fixed code that does checking if textCDFfile
   
annaffy
    Added all, all.x and all.y options to merge.aafTable
    Added custom getHTML method to aafUniGene to fix small bug

AnnBuilder
    Modification of yeastPkgBuilder to fix the bug of YEAST genename/alias
    Fixed bug in KEGGENOME url

apComplex
    Bugfix in sortComplexes
    Changed some rownames of yNameTAP

beadarray
    Improved speed of findAllOutliers and createBeadSummaryData
    Improved speed of readBeadImages
    Bugfix in createBeadSummaryData

Biobase
    Added matchpt to fnd nearest neighbours within a matrix or vector, or to match a matrix or vector onto another
    Man page updates
    Fixed subsetting of exprSet and eSet so that reporterInfo is subset correctly
    Added protections for exprSets with missing reporterInfo slots
   
biomaRt
    Converting biomaRt to use RCurl
    MySQL access is still possible, but access to BioMart databases is now by default via the bioMart webservices over HTTP
    Added drop = FALSE tot he postprocessing of getBM result in order to be consistent if there is only one attribute
   
BufferedMatrix
    New Package:
        An experimental package for dealing with large datasets
    Maintainer:
        Benjamin Milo Bolstad

cellHTS
    New Package:
        Analysis of cell-based high-throughput screens
    Maintainer:
        Wolfgang Huber

copa
    New Package:
        COPA is a method to find genes that undergo recurrent fusion
             in a given cancer type by finding pairs of genes that have
            mutually exclusive outlier profiles.   
    Maintainer:
        James W. MacDonald

gcrma
    Fixed justGCRMA to conform to the new exprSet object checking in Biobase
    Modified C code to make it C ANSI-compliant

GeneRfold
    New Package:
        Package manipulating sequences with fold routines
    Maintainer:
        Antoine Lucas

GEOquery
    Fixed GDS2eSet to comply with the new validity checking in Biobase
    Added GSElimits to getGEO to allow for parsing of large datasets in pieces

GlobalAncova
    Fixed bug regarding testing one gene
   
GOstats
    Changed GOhyperG so user can supply the universe
    Moved hyperG2Affy and hyperGtable from affycoretools
   
graph
    Fixed GXL writing for undirected graphs: no duplication of reciprocal edges
    Added GXL for all graphs in the graphExamples data and a script that can be used to recreate the rda file when class defs change
    Added 'edges' argument to initialize method fo graphNEL
    You can now create new graphNEL instances by passing a list in the 'edges' argument to initialize
    This list has the same structure as the list returned by the edges method of a graph object.
    Overhaul of integration of special edge attribute 'weight' to handle addNote, removeNode, removeEdge
    Fixed edgeData for undirected graphs
    Fixed validation of reciprocal edges for undirected graphs
    Fixed directed graph example
    Refactored addNode for graphNEL
    Refactored graphNEL initialization; made edgeL polymorphic
    We now accept two structures for edgeL; a list similar in structure to that returned by edges(g) and a more compicated nested structure documented for edgeL
    Fixed initialization of edgeL argument vector in randomGraph and randomNodeGraph
    Fixed randomGraph so weights argument works   
    Added C code for attrDataItem access to speed up read access
   
iSNetwork
    Added functionality to link plots of a graph
    Started a vignette


iSPlot
    Added a paper to the package
    Updated man pages
   
makePlatformDesign
    Bugfix in readSNPCDF and readSNPtxtCDF to correctly label PM and MM probes
    Added posfile option in makePDpackage; useful for NGS data, in order to update the probe positions using a .pos file
    Added dependence on affyio

MVCClass
    Added a slot to the graphView class
   
oligo
    Bugfixes in image and boxplot and normalize.quantiles
    Added dependence on affyio
    Fixed a bug for affy expression arrays

RMAGEML
    Added help file for getSubmitterAddress function
   
ScISI
    Added checkComplex to check protein complexes inclusion within the ScISI and a new data set
    Updated the constructScISI file so that it generates datasets and saves them to a directory of choice
    Added a vignette that explains the creation of the interactome
    Added functions to calculate all graph stats as well as a vignette

sizepower
    New Package:
        This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study.
        The user is referred to the cited references for technical background on the methodology underpinning these calculations.
        This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice
    Maintainer:
        Weiliang Qiu
snapCGH
    Changed optimizer from Nelder-Mead from praxis to increase stability of results
    Changed plotSegmentedGenome to accept more than one SegList object
    Removed code replication with aCGH package
    Added arguments to runDNAcopy allowing all the available parameters to be set
    Added 'seed' argument to sim.structure to allow reproducible results
    Made the default information about chromosome length into megabases rather than base pairs
    Removed unneeded argument 'maxiter' from fitBioHMM
    Changed plotSegmentedGenome to make chromosomal segments consisting of a single clone more obvious
    fitBioHMM now computed the distance between clones automatically
    Fixed bug in fitBioHMM where selecting BIC as the criterion caused a crash
   
SNPscan
    New Package:
        This package contains methods for visualization of SNP chip data
    Maintainer:
        Robert Scharpf

xcms
    EIC width can now be specified in diffreport
    Better error reporting in getEIC