January Changes in BioC Devel

    January 2007

affxparser
    Added convertCel() and compareCels()
    Added argument 'writeMap' to updateCel()
    Bugfix: Using argument 'readMap' in readCel() would give an
    error
    Now readCdfUnits(..., readDirections = TRUE) also returns unit
    group directions
    Added cdfAddPlasqTypes()
    Now readCdf() reads all unit and group fields by default
    Read maps can be used to unrotate CEL data rotated by dChip
    software
    Added writeCdfHeader(), writeCdfQcUnits() and
    writeCdfUnits(). These are all used by writeCdf(), and make it
    possible to write a CDF in chunks in order to, for instance,
    convertCdf() using constant memory

affy
    Added checkValidFilenames() to ensure that what is passed to
    e.g., ReadAffy() are actually celfiles, and give a reasonable
    warning if not

affycoretools
    Bug fixes to vennSelectBM(). Added code to remove illegal
    filename characters, and corrected subsetting of exprs matrix
    to result in a matrix even if it is only one row

affyPLM
    PLMset objects no longer have direct dependence on eSet
    objects (nor exprSets as done historically). Removed all
    exprSet functions or replaced with ExpressionSet equivalents

annaffy
    Added compatibility for SQLite-based annotation data
    packages. This patch allows annaffy to be used with
    environment and SQLite-based annotation packages. The vignette
    has been converted to use the hgu95av2db package for testing
    purposes

annotate
    Import AnnotationDbi, fixed lookUp() to work with SQLite-based
    packages. With these changes you can load SQLite-based
    packages such as hgu95av2db and use lookUp() with it (you
    still specify "hgu95av2", not "hgu95av2db")

annotationTools
    New Package:
        Functions to annotate microarrays and mine for
        orthologs from flat file databases (plain text files).
    Maintainer:
        Alexandre Kuhn

aroma.light
    Bug fix: averageQuantile.list() would not accept vector of
    different lengths. Thanks Alicia Oshlack

Biobase
    Fixed code in openVignette() to give a better error message
    when the installed package doesn't contain a PDF vignette
    Provided a more detailed example for read.AnnotatedDataFrame()
    Clarified ExpressionSet documentation
   
biomaRt
    Fixed bug in getBM() when output is a list
    Added getLDS() (linked data set) function which enables one to
    link two BioMart datasets and construct a combined query of
    both datasets (e.g., in homology mapping)

Category
    Fixed show() method to work on all HyperGParams objects
    instead of just GOHyperGParams objects
    Changed vignette and man pages to use hgu95av2db

cghMCR
    Bug fix that allows the code to exit gracefully when failing
    to detect any altered segments

copa
    Added summaryCopa() to ouput a data.frame of genes that have a
    certain number (or greater) of outliers
    Fixed some errors in the vignette

cosmo
    GUI for interactively constructing constraing sets has been
    moved into separate package cosmoGUI
    Functions for plotting DNA sequence logos have been moved in
    to separate package seqLogo
    Added 'maxIntensity' parameter to cosmo() to allow likelihood
    to be maximized wrt to intensity parameter as well
    Default value for 'intCrit' changed from 'eval' to 'lik'
    simScoree() now takes argument 'minOverlap' specifying minimal
    overlap between predicted and true motifs to declare a hit
    Relaxed checks on starting values for satisfying constraints
    to avoid not finding any starting values
    Uninitialized starting falues are now skipped
    Fixed bug in computing E-value for sequences wtih unknown
    characters fixed
    A number of default options have been changed on the basis of
    new simulation results:
    wCrit changed from 'eval' to 'bic'
    modCrit changed from 'eval' to 'lik'
    conCrit changed from 'pwmCV' to 'likCV'
    conTrunc changed from 100 to 90
    cosmo() now accepts a file for specifying the background
    Markov model that follows the MEME standard
    New function bfile2tmat() converts a MEME-style background
    file into a transition matrix
    New function bgModel() produces an estimate of the transition
    matrix for the background Markov model
    A useful error message is printed if input sequence file or
    background sequence file contains a sequence of length zero
   

cosmoGUI
    New Package:
         cosmoGUI allows the user to interactively define
         constraint sets that can be used by the cosmo package
         to supervise the search for shared motifs in a set of
         DNA sequences. The constraints can be either adapted
         from a set of commonly used templates or defined from
         scratch.
    Maintainer:
        Oliver Bembom

DynDoc
    Fixed Vignette class definition. The Vignette class was using
    a non-existent VersionNumber class for one of its slots. For
    now, we'll use the version number class defined in base as s3
    'package_version'
    Fixed show() methods for SweaveOptions(), codeChunk(), and
    chunkList()
   
exonmap
    New Package:
        Provides high level functions for reading Affy .CEL
        files, phenotypic data, and then computing simple
        things with it, such as fold-changes t-test and so
        on. Applies fine grained genome-wide annotation to the
        data.

    Maintainer:
        Michal Okoniewski

genefilter
    Added AnnotationDbi to genefilter imports. This is required to
    integrate SQLite-based annotation data packages. By importing,
    we get the AnnotationDbi defined environment API functions
    such as mget() to do the right thing when the data map is an
    S4 class instead of an environment

GeneticsDesign
    New Package:
        This package contains functions useful for designing
        genetics studies, including power and sample-size
        calculations.
    Maintainer:
        Weiliang Qiu

GOstats
    Improved plotTermGraphs(). Use GO term names in the plot
    insead of GO IDs. This can be toggled using use.terms, but
    default is TRUE. We also show x/y for each node, which is the
    number from the selected list over the number in the category
    Changed the default for summary(GOHyperGResult) to use
    htmlLinks=FALSE at the command line for readability
    Refactored result plotting. Return graph objects instead of
    each helper function producing a plot. Then a single plot
    helper function plotGOTermGraph() can be used to produce a
    nicely labeled plot
    Fixed coloring of plotGOTermGraph() to shade only significant
    nodes. Nodes for which we did not test are labeled with
    0/?. Colors can be specified

graph
    Improvements to vignette
    Moved edgeL-method for distGraph and clusterGraph from
    Rgraphviz to graph

LBE
    New Package:
        LBE is an efficient procedure for estimating the
        proportion of true null hypotheses, the false
        discovery rate (and so the q-values) in the framework
        of estimating procedures based on the marginal
        distribution of the p-values without assumption for
        the alternative hypothesis.
    Maintainer:
        Cyril Dalmasso

limma
    Old functions designed to read image data files into
    data.frames are now deprecated. This affects read.matrix(),
    rg.series.spot(), read.series(), m.spot(), a.spot(),
    rg.spot(), rg.quantarray(), rg.genepix()
    wtVariables() renamed to namesInFun()
    New argument 'other.columns' for read.imagene()
    User's guide sections on spot quality weights and quality
    assessment expanded
    normalizeForPrintorder(plot=TRUE) now produces no output to
    agree with the documentation
   
lumi
    New Package:
        lumi R package is designed to preprocess the Illumina
        microarray data. It includes functions of Illumina
        data input, quality control, variance stabilization,
        normalization and gene annotation.
    Maintainer:
        Pan Du       

rHVDM
    New Package:
        A R implementation of HVDM (Genome Biol 2006, V7(3)
        R25)
    Maintainer:
        Martino Barenco

seqLogo
    New Package:
        seqLogo takes the position weight matrix of a DNA
        sequence motif and plots the corresponding sequence
        logo as introduced by Schneider and Stephens (1990).
    Maintainer:
        Oliver Bembom

SLqPCR
    New Package:
        Functions for analysis of real-time quantitative PCR
        data at SIRS-Lab GmbH
    Maintainer:
        Dr. Matthias Kohl

topGO
    New Package:
        topGO package provides tools for testing GO terms
        while accounting for the topology of the GO
        graph. Different test statistics and different methods
        for eliminating local similarities and dependencies
        between GO terms can be implemented and applied.
    Maintainer:
        Adrian Alexa

vsn
    Added a function for visualization of the loglikelihood
    Added functions for reference normalization