October Changes in BioC Devel

      October 2005

affy
    Fixed bug in read.affybatch reading gzfiles on Windows
   
affycoretools
    Added zzz.R to put vignette in Rgui menubar
    Added function hyperG2Affy to output Affy probe IDs associated with 'significant' GO terms
   
AnnBuilder
    Produce *QCDATA.Rd
    Remove 'build' in GP
    Changed the 'Category' error in GO documentations - GO changed 'Category' to 'Ontology'
    Annotate is now suggested by GO package because GOterm is defined in annotate
    Added passive option to download option - based on a patch from Denise Mauldin
    allows wget ftp functionality behind some firewalls. Default is FALSE
   
annotate
    Corrected and shortened useDataPkgs vignette
    Made installDataPackage defunct
       
applera
    New Package:
        The package supplies some basic tools for Applied Biosystems microarrays AB1700 data analysis and quality controls
    Maintainer:
        Francesca Cordero

Biobase
    Added a new example exprSet object 'exSet', which is a better example than existing 'eset'
    Modified vignettes to use exSet
       
biomaRt
    Added strand as output of getGene function
    Made data.frame the default output of getGene, getOMIM, getGO and getINTERPRO

DNAcopy
    Vignette changed to include improvements to the package such as the hybrid algorithm

graph
    Fixed self-loop bug in numEdges
    Fixed graphAM's matrix specific implementation
    Fixed a bug where subGraphs were not maintaining edgemode status
   
hexbin
    Added trellis function to hexbinplot
    Added hexplom function
    Added panel.hexboxplot for use with lattice
    Added panel.hexpose
   
hypergraph
    Fixed bug in toGraphNEL
    Hyperedges now have default labels if not specified
    Added label<- method for Hyperedge objects
    Added convenience functions hyperedgeLabels and l2hel
       
limma
    Updated userguide.pdf
    Updated kooperberg to accept RGList - old function moved to kooperberg_old
    Updated read.maimages to use colClasses argument - courtesy of Marcus Davy
    New path argument and slighely changed output names for plotMA3by2
    Fix to normexp.m2loglik to prevent infinite likelihoods
    Fix to normexp.fit to prevent non-positive alpha
    normalizeMedianDeviations and normalizeMedians replaced by normalizeMedianAbsValues
    Default methof for normalizeBetweenArrays changed to 'Aquantile'
    Update kooperberg functions - removed unnecessary Block argument for varaux1 and varaux2
    read.maimages(source="genepix.custom", verbose=TRUE) outputs bg correction method
    Calls to statmod:randomizedBlockFit changed to statmod:mixedModel2Fit
    Removed deprecated dupcor.series function
    Bugfix in merge.RGList and merge.MAList
    kooperberg now gives informative error message if input not RGList
   
MANOR
    New Package:
        We propose importation, normalization, visualization, and
        quality control functions to correct identified sources
        of variability in array-CGH experiments.
    Maintainer:
        Pierre Neuvial and Philippe Hupé

MantelCorr
    New Package:
        Computes Mantel cluster correlations from a (p x n) numeric
                 data matrix (e.g. microarray gene-expression data).
    Maintainer:
        Brian Steinmeyer

maSigPro
    New package:
        maSigPro is a regression based approach to find genes for which there are significant gene expression profile
        differences between experimental groups in time course microarray experiments.
    Maintainer:
        Ana Conesa and Maria José Nueda

matchprobes
    Fixed getProbeDataAffy to accept header change in Affy probe files
   
OptionalTyping
    New Package:
        A prototype for a mechanism for specifying the types of parameters and the
           return value for  an R function. This is meta-information that can be used to generate
           stubs for servers and various interfaces to these functions. Additionally, the arguments
           in a call to a typed function can be validated using the type specifications.
           We allow types to be specified as either
              i) by class name using either inheritance -  is(x, className),
                 or strict instance of - class(x) %in% className, or
             ii) a dynamic test given as an R expression which is evaluated
                at run-time.
           More precise information and interesting tests can be done via ii), but it is harder to
           use this information as meta-data as it requires more effort to interpret it
           and it is of course run-time information. It is typically more meaningful.
    Maintainer:
        Duncan Temple Lang

panp
    New Package:
        A function to make gene presence/absence calls based
        on distance from negative strand matching probesets (NSMP)
        which are derived from Affymetrix annotation. PANP is applied
        after gene expression values are created, and therefore can be
        used after any preprocessing method such as MAS5 or GCRMA, or
        PM-only methods like RMA. NSMP sets have been established for
        the HGU133A and HGU133-Plus-2.0 chipsets to date.
    Maintainer:
        Peter Warren

pathRender
    New Package:
         build graphs from pathway databases, render them by Rgraphviz
    Maintainer:
        Li Long

plier
    affinities code patch
    Fixed affinities memory management problem
   
prada
    Missing generics are now imported from Biobase namespace
   
rdxml
    New Package:
        This package includes a tool to convert existing
                Rd files into XML files, a GUI tool to facilitate the
                creation of R documentations in XML, and a tool to render
            XML-based R documentations into HTML.
    Maintainer:
        Nianhua Li
reposTools
    Deprecate the develOK argument to install.packages2 - end users now need devel R for devel BioC packages
   
rfcdmin
    Addition of BCCRC data to illustrate new rflowcyt functions
   
rhmetis
    New Package:
        R Interface code to the hMETIS 1.5 hypergraph partitioning library
    Maintainer:
        Seth Falcon

RLMM
    New package:
        A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays.
        Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data.
        RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization.
        This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.
    Maintainer:
        Nusrat Rabbee and Gary Wong

RMAGEML
    Fixed bug in conversion of JNI strings to C strings
    GUI fix for Windowssimpleaffy
    Fixed cex argument in plot.qc.stats which was not functional
   
simulatorAPMS
    New Package:
        Functions to computationally simulate the AP-MS technology based on wet-lab data.
    Maintainer:
        Tony Chiang

stam
    Fixed a bug in stam.threshpreds

tilingArray   
    Corrected transcription status of uORFs, to keep them from interfering with the discovery of novel transcripts
    UTR/GO association now uses only poly-A data
    Corrected bug in getGO function
    Updated GO analysis of antisense
    Slightly darker colors for segment boundaries in plotAlongChrom
    writeSegmentTable now produces nicer heading
   
vsn
    Fixed a bug that occurred for nchoosek(m, m)