April Changes in BioC Devel

    April 2007

ACME

    Fixed chi-square calculation a bit to be actual counts in the
    cells rather than the counts of the marginals in a couple of
    cells.

    Fixed bug in write.sgr when colnames were not defined on vals


affy

    Added 'cdf' argument to xy2indices() and indices2xy() so those
    without an AffyBatch can still map things. The cdf argument in
    this case is simply the name of the requisite cdf package.

    
affycoretools

    Bugfix to vennSelect() when the number of probesets == 1


affyio

    Fixed issue with non-square cel file parsing using binary (xda)
    format cel files.  The Affymetrix documentation is
    inconsistent with the reality (rows, cols swapped).


annaffy
    
    Fixed GO links


AnnBuilder

    Updated AnnBuilder to accommodate the changes to KEGG website.

    Added support for Bos taurus and fixed parsing routine for
    GENENAME

annotate

    Fixed GO helper functions to deal with missing NA entries.

    Use sample.ExpressionSet data for Pretty Output vignette

AnnotationDbi

    Changes to demo vignette to compare env and SQLite based
    annotation packages

    Add a revmap method for environment objects This allows revmap
    to be used on environment-based ann pkgs

    Added man pages for 'db_conn' and 'db_file' to HGU95AV2DB
    template

beadarray

    Changed readBeadSummaryData to read BeadStudio V2 output

    CreateBeadSummaryData now assigns array names to the columns
    of the intensity data - 'pData' and 'phenoData' now defined
    for BeadLevelList - added 'targets' argument to qcPlots and
    updated man page

bgx

    New Package:
        Bayesian integrated analysis of Affymetrix GeneChips

    Maintainer:
         Ernest Turro


Biobase

    listLen now returns an integer vector (rather than numeric)
    and I also tried to better the documentation

    Further refinement of listLen In package code, INTEGER() is a
    function, so it is better to call it only once. Also improved
    the error message to give more information and added some
    detail to the man page.

    Add ScalarCharacter class This is a utility class that can be
    used to ease validation burden when writing classes that
    require a string slot.

    Add assayDataElement<- function

    Add readExpressionSet, deprecate read.exprSet, read.phenoData

    Changed welcome message

biocGraph

    New Package:
        This package provides examples and code that make use of
        the different graph related packages produced by
        Bioconductor.

     Maintainer:
        Li Long

biomaRt

    Fixed listAttributes function

    Removed array argument from getGene, getFeature and getGO as
    affymetrix arrays can now be specified using the type argument
    of these functions. Removed to.array and from.array arguments
    from getHomolog function as the affy arrays can be specified
    using the from.type and to.type arguments. To extend the
    possible types of identifiers that can be used for the
    getGene, getGO,etc functions, the value for the type argument
    has to be a filter given by the listFilters function.

    Updating handling of BooleanFilters. Whenever the user now
    uses a boolean filter a value of 1 or 0 will have to be
    specified to indicate true or false. To see if a filter is
    boolean the user can run listFilters with the showType
    argument = TRUE.

    Slimmed the listDatasets function, and it now returns a
    dataframe with character columns rather than factors

    Added specification of the web server port. Two new BioMarts
    don't use the default port 80 and were not accessible before
    this fix.

    Rewrote XML parsers to make code cleaner. Added detection of
    filter options. Some filters have a predetermed set of values
    and now these can be shown using the filterOptions
    function. Added the function filterType so users can determine
    the type of a filter (is important to know which filters are
    booleans). Updated vignette with the two new functions.

Biostrings

    Replaced slots "start" (integer), "end" (integer) and "desc"
    (character) by single slot "views" (data frame with cols
    "start", "end" and "desc") in "BStringViews" class definition
    
     Added the matchProbePair() function

     Made matchProbePair() a new generic instead of a
     function. Default for 'baseOnly' arg in alphabetFrequency()
     is now FALSE instead of TRUE. Deprecated as.complex() in
     favor of toComplex()

BufferedMatrix

    Changed median.polish.summarize.BufferedMatrix to
    median.polish.summarize

Category

    Expose makeChrBandGraph. This patch also fixes the root node
    so that it does not contain all annotations.

    Add chrBandInciMat and makeChrBandInciMat functions

    Add geneIdsByCategory and doc

    Move sigCategories to Category and make it a generic

    Fix bug in hyperGTest for ChrMapHyperGParams objects R's
    intersect(x, y) function returns a vector with mode matching y
    if x and y have different modes. The bug was the result of
    assuming that standard coerce rules apply. They don't in this
    case as is documented in the intersect man page.

cellHTS
    
    Fixed a bug in the read function (that didn't seem to have an
    effect in previous R versions), and made the verbose output a
    bit prettier

copa

    Small change in copaPerm() that speeds the operation by about
    a gazillion-fold. Thanks to Laurent Gaultier for pointing this
    out.

CORREP

    New Package:
        Multivariate correlation estimation and statistical
        inference. See package vignette.

    Maintainer:
        Dongxiao Zhu


DNAcopy

    Added code to not split if maximal statistic is small (<= 0.1)
    and split if it is large (>= 7) without computing the
    p-values.

    Added warning that windowing code wil be deprecated in version
    1.11

flowCore

    Updated Subset for new multiple filter options. Also fixed
    filterSummary

    Big changes to HowTo vignette. * Minor changes to coercion and
    read.flowSet to address Errol's troubles. * Removed as()<-. I
    guess Seth will be happy. * Minor documentation changes * A
    couple of small bugs with split * A $ accessor for flowSets

GEOquery

     Updated GDS2eSet to return an object of class ExpressionSet
     instead of the old exprSet

    
GOstats
    
    Fixup and document termGraph, inducedTermGraph, and
    plotGOTermGraph

    Fixed up the compGdist function a bit

    Modification to probeSetSummary() to allow end users the
    option of passing a vector of probeset IDs so the output of
    this function actually counts _all_ probesets that contributed
    to a significant GO term.

graph

    Fix subGraph attribute handling for graphNEL This needs to be
    generalized for all subGraph methods. This patch adds proper
    handling of node and edge attributes for the subGraph
    operation.  Before, we copied all attributes and now we only
    copy over the appropriate subset.

    Fix documentation of graphNEL class

    addEdge for graphNEL warns if edge already exists Note that
    for graphAM, this is an error. We warn when replacing an
    already existing edge using addEdge because in the past some
    users used graphNEL for representing non-simple graphs with
    multi-edges. Since this is no longer supported, a warning
    message is helpful.

limma

    limma 2.9.17 - bug fix to read.maimages() for
    source="arrayvision". Now reads arrayvision files again for
    the first time since version 2.3.1.

makecdfenv

    Modified make.cdf.packages() to create an additional
    environment with the usual package name appended with 'dim'
    (e.g., hgu95av2dim) that contains the chip dimensions. This is
    intended to be used by indices2xy() and xy2indices() in the
    affy package as a replacement for the deprecated xy2i() and
    i2xy() functions.

Mfuzz

    Bug in mfuzz.plot2 fixed

pcaMethods
    
    Added a svd method that is robust to outliers. Also a pca
    method based on this robust svd.

    Added vingette discussing handling of data with outliers

    nipals(center=T) was also accidentially sclaing the data, as
    we used scale(data, center=T).  This has been fixed.
    
    svnImpute returned too many scores/loadings, this was
    fixed. And now we also assign correct row/column names to
    scores/loading matrices

prada

    Fixed bug in drawGate when adding additional regions

puma

    New Package:
        Most analyses of Affymetrix GeneChip data are based on
        point estimates of expression levels and ignore the
        uncertainty of such estimates. By propagating uncertainty
        to downstream analyses we can improve results from
        microarray analyses. For the first time, the puma package
        makes a suite of uncertainty propagation methods available
        to a general audience. puma also offers improvements in
        terms of scope and speed of execution over previously
        available uncertainty propagation methods. Included are
        summarisation, differential expression detection,
        clustering and PCA methods, together with useful plotting
        and data manipulation functions.

     Maintainer:
         Richard Pearson

reb

    Added movt() - a moving t-test method for reb()

Rgraphviz

    deprecate imageMap

    rename LLagopen to agopenSimple

RWebServices

    Provide more informative error messages when Java -> R data
    tests go wrong

    Add indexNA in RComplex and RNumeric, and modify convert
    functions correspondingly. We tried to use NaN to represent
    both NaN and NA for R complex and R numberic vectors in
    Java. Now we seperate those two concepts. * change the java
    class name that represents all functions in a package from
    <package>.java to <package>Function.java

siggenes

    EBAM updated, added new vignette

    Posterior probabilities are truncated at zero

tilingArray
    
    Updated function segChrom and segmentation vignette

    
xcms

    Modified findPeaks method: - Moved column "i" (peak number
    within combined EIC) to the second-to-last column - Added
    column "sn" with signal to noise ratio xcmsSets now include
    "i" and "sn" columns in the peaks matrix

    Added : - rawEIC method - findMZBoxes method -
    findPeaks.centWave method Modified findPeaks() method to
    support different findPeaks.* algorithms

    Added some lines concerning findPeaks.centWave to the
    vignette, changed output of centWave to matrix instead of
    data.frame

    Removed formerly deprecated function clustunique() Changed
    xcmsEIC plotting function from an S4 to an S3 method Removed
    all instances of isGeneric()