November Changes in BioC Devel

    November 2006

affxparser
    Bugfix for readCdfUnits() with stratifyBy="mm", which
    previously returned pm probes
   
    Bugfix for readCdfGroupNames() which was crashing on Unix

    Added stratifyBy argument to readCdf()
   
affy
    Changed output from exprSet-based objects to ExpressionSet-based objects

affycoretools   
    Added ability to plot arbitrary principal components in plotPCA()

    Added hyperGoutput(), a replacement for the hyperG2annaffy()
    function that uses new functions in GOstats/Category package

affyio
    Added gzipped binary cel file support

affyPLM
    Added standard error output to the RMA model

affyQCreport
    Added lattice dependency

AnnBuilder
    egRefseqParser() modified to skip entries with a missing value
   
    Turned off warning message for mis-matched KEGG file names as
    a given organism may not have all the pathways

Biobase
    Changed makeExpressionSetPackage() to makeDataPackage() with
    an ExpressionSet method

    Added Biobase dependency

biomaRt
    Import RCurl, removed RMySQL from suggests

    Enabled query for data coming from more than two tables when
    using biomaRt in MySQL mode

    Added check to see if the server is down when a query returns
    an empty result

    Updated biomaRt to work with new BioMart v0.5 release

Biostrings
    Renamed 'first' and 'last' slots to 'start' and 'end' in
    BStringViews class

BSgenome
    Instead of having all sequences stored in BStringViews
    objects, now single sequences are stored in DNAString objects,
    and multiple sequences are stored in BStrinbViews objects. As
    a consequence, the definition of the BSgenome class has been
    changed and the show() method prints two separated indices

    Fixed bug in buildDataFiles()
   
    Added getSeq() function

    Added the available.genomes() function

BufferedMatrix
    Added ability to use logical vectors to index BufferedMatrix
    objects

    Registered the C-level functionality so it can potentially be
    used in other packages

BufferedMatrixMethods
    New Package: Provides microarray related methods that utilize
    BufferedMatrix objects

    Maintainer: Benjamin Milo Bolstad

Category
    Integrated hyperGTest() to use KEGG and PFAM as well as GO terms

    Fixed htmlReport() to use the label argument

    Use appand=FALSE in the definition of the generic of htmlReport()

    Added DBPkg class for SQLite-based annotation packges
   
    Added various functions for SQLite-based annotation packages

cosmo
    New Package: cosmo searches a set of unaligned DNA sequences for a shared
    motif that may, for example, represent a common transcription
    factor binding site. The algorithm is similar to MEME, but
    also allows the user to specify a set of constraints that the    
    position weight matrix of the unknown motif must satisfy.
    Such constraints may include bounds on the information content
    across certain regions of the unknown motif, for example, and
    can often be formulated on the basis of prior knowledge about
    the structure of the transcription factor in question.
    The unknown motif width, the distribution of motif occurrences
    (OOPS, ZOOPS, or TCM), as well as the appropriate constraint
    set can be selected data-adaptively.

    Maintainer: Oliver Bembom

GOstats
    Code for htmlReport() moved from GOstats to Category

    Bugfix to probeSetSummary() which was failing due to move of
    functions to Category

KEGGSOAP
    Updated to access KEGG API v6. Added functions
    search_compounds_by_name, search_glycans_by_name,
    search_compounds_by_composition,
    search_glycans_by_composition, search_compounds_by_mass,
    search_glycans_by_mass, search_compounds_by_subcomp,
    search_glycans_by_kcam

made4
    Bugfix to bga(), which errored on certain Affy probeset names

occugene
    New Package: Statistical tools for building random mutagenesis
    libraries for prokaryotes. The package has functions for
    handling the occupancy distribution for a multinomial and for
    estimating the number of essential genes in random transposon
    mutagenesis libraries.

    Maintainer: Oliver Will

pdInfoBuilder
    New Package: This package produces SQLite-based cdf/annotation
    databases for SNP chips. It can be extended for handling other
    chip technologies
   
    Maintainer: Seth Falcon

RefPlus
    New Package: The package contains functions for pre-processing
    Affymetrix data using the RMA+ and the RMA++ methods.

    Maintainer: Kai-Ming Chang

SemSim
    New Package: Implementation of semantic similarity measures
    based on information content of Gene Ontology terms.

    Maintainer: Xiang Guo

smoothMiner
    New Package: use smooth regression to investigate families of
    trajectories

    Maintainer: V. Carey