April Changes in BioC Devel

    April 2006

affxparser
    Updated fusion SDK
    Added argument 'reorder' to readCel() and readCelUnits(), which will reorder cell indices in order before reading CEL data
    Added C code for readCdfCellIndices() to speed things up
    New methods invertMap(), readCdfCellIndices() and readCdfUnitsWriteMap()
    Bug fix - Arguments '...' to readCelUnits() was passed to two internal functions, instead of one
   
affy
    Changed rma() so it returns an empty matrix in the se.exprs slot
    Fixed warnings when using smoothScatter in MAplot
   
affycoretools
    Bugfix in plotPCA()   

affyio
    Added configuration files so ZLIB is properly detected and defined
   
affyPLM
    Better summary() function for PLMset objects
    Added functionality for reading binary format expression value output from RMAExpress
    Added 'density' as an option of NUSE and RLE
    Added 'quantile.robust' as normalization option in fitPLM(), threestep() etc

annotate
    Added pmid2MIAME()
    Fixed a number of things for KEGG2heatmap() and GO2heatmap()
   
AnnotationDbi
    New Package:
        Provides user interface and database connection code
        for annotation data packages using SQLite data storage.
    Maintainer:
        Seth Falcon

apComplex
    Converted graphNEL to new graph class definition
   
arrayQuality
    Fixed bug in meeboQuality control boxplots
    Fixed bug in spike.sensitivity + legend of dot plot
   
Biobase
    Many changes to eSet object
        New class AnnotatedDataFrame to contain phenoData information
        New class union AssayData to abstract data in asayData slot. Data can be stored as elements of an environment, list, or 'lockedEnvironment'
        (an environment which is copied when data are modified; this is meant as a space-efficient way to pass large read-only data to functions)
        New class hierarchy eSet (Virtual), ExpressionESet (Virtual), ExpressionSet, exprSet replacement GeneralizedExpressionSet, SnpESet (Virtual), SnpSet
        An exprSet can be updated with as(exprSet, "ExpressionSet")
        An eSet can be updated to GeneralizedExpressionSet with updateOldESet(eSet)
    Renamed GeneralizedExpressionSet as MultiExpressionSet
    Narrowed signature of some setReplaceMethods to reflect the expected data type of replacement values
    Initial documentation for eSet-derived classes
    Simplified eSet class structure to eSet (Virtual), ExpressionSet, SnpSet
    Deprecated unused phenoData methods getUnits() and addVarMetadataEntry()
    Switched to use message() instead of cat() for banner message - this allows end users to suppressMessages() if so desired
    Added examples for eSet and ExpressionSet
    Refactored cache(), and changed usage. You now call cache like this: cache(foo <- {...}). Optional arguments dir and prefix are now available to control the location and naming of cache files
   
biomaRt
    Fixed bug in queryGenerator(), limit on number of allowed tables to join in query was wrong
    Added a vignette 'prettyOutput' that shows how to use biomaRt and annotate functionality to make nice annotated HTML tables
    Update for getFeature() method - filter chrom_name became chr_name in ENSEMBL
    Fixed bug in parsing of BioMart registry
    Adapted convenience functions to work with ENSEMBL 37 and 38. ENSEMBL 38 will be released soon.
   
Biostrings
    Added the letter() function
    Added two matchPattern and countPattern methods for character vectors or BStringViews objects
    Improved help pages and vignettes
    Implemented alphabetFrequency in C
    Put reverseComplement() function back in

BufferedMatrix
    Improved ewApply(), added colApply(), rowApply(), as.matrix()
   
Category
    Added show method for GeneGoHyperGeoTestParams()
    Fixed bug encountered when GO mapping has an ID where the ontology info is NA
   
cghMCR
    Functions for plotting MCRs added
    Added example source data
   
DNAcopy
    Increased speed by adding a stopping boundary to declare change early
    Bug fixed in plot.DNAcopy()
    Expanded vignette
    Added cytoband data
    Fixed subset command which gave samples in the original order only
   
GenomeBase
    New Package:
        Meta information about the different genome data packages
            and objects shared by these packages
    Maintainer:
        Herve Pages

GlobalAncova
    Completely new version

graph
    Fixed bug in removeEdge() with a graphNEL
    Added missing coerce method from graphNEL to graphAM
    Fix to IMCAGraph, now passes validGraph

iSNetwork
    Added identifyView methods and added a new heatmap function that will be interactive
   
limma
    New function plotFB()
    read.maimages() no longer tries to guess ndups for GenePix data
    Changes to the argument list and defaults for geneSetTest() to make it more intuitive
    In fitFDist(), the bounding of standard deviations away from zero now uses a smaller bound
    New generic function avedups(), with methods for default and MAList objects
    read.maimages() now uses readGenericHeader() to get skip and column names for generic source files
    readGenericHeader() now uses protedtMetachar() so that special characters can be used in column headings
    Improved man page for topTable
    Fixed read.maimages(), which was setting RG$ngrid.c incorrectly when source = "genepix" and the metagrid layout could not be determined
    Package to analyze Yeast 2-Hybrid Data Sets

logicFS
    New Package:
        Identification of interactions between binary variables using LogiC
        Regression. Can, e.g., be used to find interesting SNP interactions. Contains
        also a first basic bagging version of logic regression for classification.   
    Maintainer:
        Holger Schwender

LPE
    Added an option for Bonferroni adjustment
    Changed the name of mt.rawp2adjp() to mt.rawp2adjp.LPE() to avoid collisions with multtest function of the same name
       
maanova
    Changed maintainer to Lei Wu
    Instead of pooled p-value, p-value based on subset method is implemented in matest.R. Include option critical.
    Version number jumps from 0.98.8 to 1.2.0 on CRAN in order to keep up with bioconductor version number.
    Add comments in matest() help page about test covariate in "contrast" and "test type" section.
   
made4
    Bug fix to plotarrays()
   
makecdfenv
    Added species argument to make.cdf.package() as well as modifications to DESCRIPTION file to accomodate biocViews for the cdf packages
    Changed instantiation of environments to use new.env(hash = TRUE, parent = emptyenv()) to correspond to deprecation of NULL environments in R-2.3.0
    Changed maintainer to James W. MacDonald

makePlatformDesign
    Added documentation for release
    Fixed sequence of character for NDF and BMAP files
    Fixed to work with new eSet classes
    Fixed bug concerning the identification of NimbleGen arrays
    Fixed bug for tiling arrays
   
matchprobes
    Added species argument to makeProbePackage() as well as modifications to DESCRIPTION file to accomodate biocViews for the probe packages
    Switched to parent = emptyenv() for calls to new.env()
   
metaArray
    NA/NaN/Finite check enhanced for all parameters
    Sampling scheme for alpha modified to meet the identifiability constraints
    T/F changed to TRUE/FALSE

MVCClass
    Changed some man pages and required Biobase
    Changed two slots in sPlotView class from colx and coly to xvar and yvar to match documentation
    New method identityView()
   
oligo
    Added basecontent from matchprobes
    Many documentation additions/fixes
    Adaptations to work with new eSet class
   
ontoTools
    Many changes to get in line with new annotation resources
    Removed obsolete metaData
   
OrderedList
    New Package:
        Detection of similarities between ordered lists of
        genes. Thereby, either simple lists can be compared or gene
        expression data can be used to deduce the lists. Significance
        of similarities is evaluated by shuffling lists or by resampling
        in microarray data, respectively.
    Maintainer:
        Claudio Lottaz

prada
    Now using the MultiExpressionSet subclass
    Changed to use ddCtSet subclass instead of MultiExpressionSet for storage of RT-PCR data and results
    Fixed bug in validator function for ddCtSet
   
RMAGEML
    Fixed bug in determining unique array identifiers in dataset
   
simpleaffy
    Added porcine arrays to qc data tables
    Fixed doc bugs in get.array.indices()
   
simulatorAPMS
    Added a help page for filteredProt()
   
SNAData
    Converted serialized graphNEL to new class definition in graph
   
tilingArray
    Added affy dependence
    Updated readCel2eSet() to use the ExpressionSet class

y2hStat
    New Package:
        Package to analyze Yeast 2-Hybrid Data Sets
    Maintainer:
        Tony Chiang