March changes in BioC Devel

    March 2007

ACME
    New Package:

        ACME (Algorithms for Calculating Microarray Enrichment) is
        a set of tools for analysing tiling array ChIP/chip, DNAse
        hypersensitivity, or other experiments that result in
        regions of the genome showing "enrichment".  It does not
        rely on a specific array technology (although the array
        should be a "tiling" array), is very general (can be
        applied in experiments resulting in regions of
        enrichment), and is very insensitive to array noise or
        normalization methods.  It is also very fast and can be
        applied on whole-genome tiling array experiments quite
        easily if enough memory is present.

     Maintainer:

        Sean Davis

affxparser

    Added argument 'truncateGroupNames' to readCdfGroupNames()
    which defaults to TRUE. When TRUE, any prefix of group names
    identical to the unit name will be stripped of the group
    names.

affy

    updateObject() now removes empty or inconsistent se.exprs from
    AffyBatch objects

    Return new('matrix') rather than NULL if se.exprs undefined

   
AnnBuilder
   
    Updated GO url, fixed bug in getGOUrl()

   
annotate

    Added getAnnMap() and annPkgName(). getAnnMap() provides a
    single interface for retrieving map objects from both SQLite
    and environment-based annotation data packages. AnnPkgName()
    is a simple helper that returns the package name given chip
    and package type (db or env)

    Add aqListGOIDs() to list GO IDs in specified ontologies
   
    Changed default behavior of getAnnMap(). The default value of
    load is now TRUE. If type is missing then we use the first
    matching package on the search path and only then fall back to
    loading based on the default value for type

AnnotationDbi

    Added the AnnObject and AnnTable classes. The AnnMap class
    (and its subclasses) now derive from the AnnObject class

    Added an as.data.frame() method for AnnTable objects
   
    Added the RawAnnMap class and use it in the AFFYHUEX_DB schema

    Added as.list() for RawAnnMap objects

    Added new generics toTable() and toList() as replacements for
    as.data.frame() and as.list()

beadarray

    Bugfix to qcBeadLevel() and new arg experimentName for HTML
    report heading


biomaRt

    Enabled display of attribute/filter groups and categories. A
    summary of the available groups and categories can be obtained
    with the attributeSummary and filterSummary functions. The
    main use of this is to limit the output of the listAttribute
    and listFilters functions to only selected categories or
    groups. Sequence data can now also be retrieved by the getBM
    function, the getSequence function stays alive as it might be
    easier to use for new biomaRt users.

    Updated getBM to enable retrieval of upstream and downstream
    flanking sequences of a specified length. Removed getOMIM and
    getINTERPRO functions as the same functionality is provided by
    getBM

    Added column names to output of getSequence. Fixed database
    connection for getSequence when using biomaRt in MySQL mode as
    the host to connect to changed. Fixed requestid for
    identification of biomaRt at the web service.


BufferedMatrix

    Added a basic vignette


CALIB

    New Package:

        This package contains functions for normalizing spotted
        microarray data, based on a physically motivated
        calibration model. The model parameters and error
        distributions are estiamted from external control spikes.

    Maintainer:
         Hui Zhao

Category

    Now using lgCMatrix class from Matrix package for the
    representation of the adjacency matrix instead of
    graph-NEL. This should be much more memory and time efficient

   
    Move nsFilter to genefilter package   

   
    Better handling for chrom band annotations specified as ranges
    For unexpected range formats, we now try using lcPrefix and
    use that result if there is a non-zero common
    prefix. Otherwise, we fall back to current strategy of
    grabbing just the entire chromosome part.


cellHTS

    Simplification of the Bscore function: remove the step of
    doing a log transformation within 'Bscore' function

   
EBImage

    Added 'stackObjects' to generate a stack of
    one-object-per-image images after object detection (many
    people wanted it) and 'tile' to generate a tiled image from a
    stack (e.g. to use in combination with 'stackObjects')

   
exonmap

    Added plot parameter to gene.strip

    Added splicing index, gene-exon-probeset reports and enabled
    list output from gene-transcript-exon-probeset translation
    functions

   
fbat

    New Package:
       
        This package implements a broad class of Family Based
        Association Tests for genetics data, with adjustments
        for population admixture using the code from the
        'FBAT' software program (see
        http://www.biostat.harvard.edu/~fbat/fbat.htm). Features
        include: - Uses data from nuclear families, sibships,
        pedigrees, or any combination; provides unbiased tests
        with or without founder genotypes.  - Analyzes
        dichotomous, measured, or time-to-onset traits and
        multiple traits; trait definition can be optimized.  -
        Offers bi-allelic and multi-allelic tests of
        association using standard genetic models (additive,
        dominant, recessive or genotype).  - Offers large
        sample and Monte-Carlo exact tests of the null
        hypothesis: no linkage and no association; offers
        large sample test of H0: no association.  - Estimates
        allele frequencies; checks Mendelian consistency.  -
        Tests multiple markers using haplotypes; estimates
        haplotype frequencies and linkage disequilibrium
        between pairs of markers.  - Offers two multi-marker
        tests for testing multiple markers simultaneously,
        without resolving phase or assuming no recombination.
        - Uses standard pedigree data files; phenotype file is
        optional.  - Offers the Sibs Disequilibrium Test.

    Maintainer:

        Weiliang Qiu   
       
gcrma

    Added checkValidFilenames() to justGCRMA() which ensures that
    '...' picks up celfile names only or passes back a reasonable
    error message
   
    Changed output of justGCRMA() from an exprSet to an
    ExpressionSet

    Added a 'read.verbose' argument to justGCRMA() to pass to
    read.probematrix()


GeneticsBase

    New Package:

        The R Genetics Project is a collaborative effort to
        develop a complete set of tools for storing, accessing,
        manipulating, and analyzing genetics data, from small
        candidate-gene studies consisting of a few genetic markers
        to large whole-genome studies containing hundreds of
        thousands of markers.  This package (GeneticsBase)
        provides a foundation of efficient data structures and
        easy-to-use manipulation functions.

     Maintainer:

        Gregory Warnes

graph

    Fix bug in finding the non-null dimnames in graphAM init

limma
   
     Bug fix to read.columns, to read SPOT files with a leading
     column of row numbers. Was failing because the number of
     headers was less than the number of columns.

     New tests for topTable() added to limma-Tests.R - bug fix to
     topTable(). sort="M" and resort.by="M" needed to be updated
     to sort="logFC" and resort.by="logFC". Also sort="AveExpr"
     and resort.by="AveExpr" are now allowed.

lumi
   
    Updated addNuId2lumi function to fix a bug when combining
    multiple duplicated probes.

    Make lumiN accept the ExpressionSet inherited objects and data
    matrix

    Updated lumiN.rsn to allow targetArray to be a vector or
    LumiBatch object

   
makecdfenv

    Deprecated xy2i() and i2xy()

MANOR

    Added function getChromosomeArm()

    Added intensity.flag for lowess normalisation; added
    pct.spot.before.qscore()

   
nem

    Included (1.)  functions for continuous data by Matthias
    Maneck and (2.) new inference methods by Holger
    Froehlich. Almost all functions got changed in the process.

   
oligo
   
    Started adding help pages

PGSEA

    New Package:
      
        Parametric Analysis of Gene Set Enrichment
      
    Maintainer:

        Karl Dykema

Ringo

    New Package:

        The package Ringo simplifies the analysis of two-color
        oligonucleotide microarrays from NimbleGen, which for
        example can be used in ChIP-chip projects. The package
        employs functions from various other packages of the
        Bioconductor project and provides additional
        NimbleGen-specific and ChIP-chip-specific
        functionalities. Its mainly covered subjects are data
        read-in, quality control, visualisation and
        identification of genomic regions showing enrichment
        in ChIP-chip. Please take note that Ringo is geared
        towards two-color NimbleGen microarrays. For
        single-channel NimbleGen arrays, we recommend the
        package 'oligo'.

    Maintainer:

        J. Toedling   


RWebServices

    New Package:

        This package provides mechanisms for automatic
        function prototyping and exposure of R functionality
        in a web services environment.

    Maintainer:

        Biocore Team


siggenes

    New, totally revised versions of the EBAM functions. Vignette
    has not been updated yet.


vsn

    Interface to logLik now uses default values rather than
    'missing' to decide whether to do normal or profile likelihood
    fixed man page bugs fixed documentation

    Added a method for justvsn for AffyBatch and limma RGLists