July Changes in BioC Devel

            JULY 2005

affxparser
    New package

affyQCReport
    New package

AnnBuilder
    In the function GP() in AnnBuilder/R/GP.R, remove the default argument srcUrl = getSrcUrl("GP", "human")
    to srcUrl = getSrcUrl("GP") in order to match the definition of getSrcUrl()
    Put more criteria in getKEGGBuilt() in order to determine invalid built
    Change `Vva = "Vitis vinifera"` to `Vvi = "Vitis vinifera"` in the function
    UGSciNames() of AnnBuilder/R/getSrcUrl.R
    Change GO URL from http://www.godatabase.org/dev/database/archive/latest/ to
    http://archive.godatabase.org/latest/
    Modify downloadSourceData.R in order to fit the structure change in ftp://ncbi.nih.gov
    Source URLS for UG updated
   
Biobase
    Bugfix - checking for valid names on eSets
    Added code for eSet class wo it will function with oligo package
    Accessors added for oligo package
    Added drop = "missing" to split() methods to match R-base
    New function read.phenoData() for reading phenoData objects
    New function df2pD() for converting data.frames to phenoData objects
    Added annotatedDataset class - eSet and exprSet are now subsets of this class
   
biocViews
    New package

biomaRt
    Updated package to work with Ensembl V32
    Changed default values of arguments and updated examples
    Added function to export fasta files from retrieved sequences
    Added GO as a filter in getFeature
    Fixed bug in listMarts function
   
ctc
    Added a vignette

fdrame
    New package

GeneMeta
    Modified three functions - zScores, zScorePermuted, and zScoreFDR
    Argument "classes" is checked and converted to 0/1 within each function

GeneSpring
    Fixed bug that caused the last parameter to be dropped from the expparam slot
   
GlobalAncova   
    New package

hexbin
    Added argument "n" to hexMA.loess and hexVP.loess

hopatch
    Fixed bug in makeTree so that final zeros are cut even when there is only 1 child
    Fixed bug paircollap so final medoids label has 1 not 0 if the labels do

hypergraph
    Begin integration of shared item set finding algorithm

iSNetworks
    Fixed some bugs that occurred when updating multiple points
    Also slightly changed the user interface
    Added some functionality so messages could be passed to child MVCs
   
LMgene
    New package

LPE
    Updated am.trans to ensure maximum 5 reps are used
    Various documentation and man page changes
    Updated lpe() to ensure that interpolation does not cause negative variances
    Updated baseOlig.error.step1 and baseOlig.error.step2 to eliminate NAs
   
makePlatformDesign
    Converted all sequence info to uppercase
    Fixed nrow/ncol calculation for Nimblegen chips
    Changed order for SNP chips to follow order(target_sequence, SNP, snp_location)
    Code changes to increase speed for SNP chips
    Indexing for chips starting at (1, 1) rather than (0, 0)
    Re-order feature_Info slot for PDenv

mmgmos
    New package

multtest
    Fixed density smoothing
    Fixed update method with smooth null
    Allow classlabel to be a factor in mt.teststat, mt.maxT, and mt.minP
    Fixed captions on MTP plot
   
MVCClasses
    Removed some bugs that occurred when trying to update multiple points
    May have also added some functionality for creating update child MVC messages
    Added some new functionality so messages could be passed to children MVCs
   
oligo
    Changed dependencies - Biobase 1.6.4 and R-2.2.0
    Changed pm() and mm() accessor functions to return geneNames
    Added histogram and featureIndex methods
   
pdmclass
    New package

prada
    Fixed bug in plotPlate (wrong imageMap coordinates)
    Fixed bug in readCytoSet

Rgraphviz
    Enabled the circo and fdp layout methods
    Fixed segfault with Graphviz 2.5 (and 2.6)
    Compiled Rgraphviz to work on Windows

tilingArray
    Bugfix in scoreSegments - choice of segments for UTR mapping
    Updates for better quality reports
    Renamed plotAlongChrom2 to plotAlongChrom
   
tkWidgets
    Title options added to pickItems
   

xcms
    Fixed bug in retention time correction leading to NA values



            JUNE 2005

affyPLM
    fix a problem with memory usage (varcov="none").
    fix a problem with 1 probeset probes.
    another 1 probe probeset fix (for NUSE).
    modified boxplot() for exprSets to use range=0, this makes it agree with
    default behavior for boxplot() on affyBatches.
   
AnnBuilder
    Revised egAccParser and egRefseqParser in order to grep correct
    refseq information.
    Updated Organism name requirements.
    Moved _PMID_ to _getMultCol4Yeast_ in yeastPkgBuilder.R.
    Change to version 1.6.6

annotate
    Bugfix in htmlpage() to allow lists or data.frames for othernames.

arrayQuality
    Fix dotplot when compBoxplot = FALSE.
    Bugfix to allow qpHexbin to work with release version of hexbin.
   
Biobase
    Added reverseSplit(), a function to reverse lists.
   
biomaRt
    Added new function getINTERPRO().
    First attempt at a faster and more efficient version of getGene().
    Fixed bug in getGene().
    Made getGo and getOMIM faster.
    Fixed bug in getXref().
    Updated getHomolog() to work with ensembl and Affy IDs.
    Added query to getFeature().

clusterStab
    New package

gcrma
    Removed unnecessary variables (Q and Qmm) from call to bg.adjust.fullmodel().

genefilter
    Added the rowPAUCs functions by Florian Hahne.
    Bugfix in rowtests().
    Bugfix in eSetFilter().

GeneMeta
    Added a VignettePackage to the GeneMeta vignette.

geneplotter
    Moved histStack() from prada to geneplotter.
    Bugfix in histStack() x-axis labeling.

GeneR
    writeFasta parameters reordered + minor changes in default parameters of assemble + new
    option upper = TRUE for readSeq() and readFasta() + unionSeq() has now
    only one parameter.

ideogram
    Added na.color argument to ideogram().
   
iSNetwork
     Made revisions to deal with new methods for messaging within a MVC object.
   
MVCClass
    Added methods for messaging within a MVC object.
   
prada
    plotPlate() now using grid graphics.
    fixed subsetting bug in replaceMethod() for cytoFrame.
    added plot method for cytoFrame.
    API changes to fitNorm2().
    fitNorm2() now accepts cytoFrames as input.

Resourcerer
    Parameter names added to the call to ABPkgBuilder to avoid confusion.
   
Ruuid
    changed configure.in to use pkg-config if no glib-config is found.
   
tilingArray
    Fixed the counting of ncRNA.
    Updates to all scripts according to Lar's suggestions
    New function overlappingFeatures().
    scoreSegments() now makes overlapFeatAll, nicer plotAlongChrom2.
    GO categorization of candidate antisense-regulated genes.
    Fixed feature labeling bug in plotAlongChrom2()
    Added hypergeometric testing for GO classes, removed obsolete antiSense.R
    Nicer color scheme for plotAlongChrom2.
    Added showDens, table-ncRNAs, writeSegmentTable, bugfix in tableSegments.R

vsn
    Updated documentation following comments by Axel Rasche.