June Changes in BioC Devel

    June 2006

ABarray
    New Package:
        Perform gene expression analysis with Applied Biosystems
        Gene Expression data format
    Maintainer:
        Yongming Andrew Sun

affxparser
    Added updateCel() which can update 'intensities', 'stdvs', and/or 'pixels' for all or a subset of the cells in binary CEL files
   
affy
    Small changes in how mas5 background is computed, that improve the agreement between mas5() and the output from Affymetrix's software
    Fixed problem with how statistics are plotted if xlim is supplied to MAplot
    More control over how the MAplot gets plotted including control of the plotting character and loess line
   
affyPLM
    Fix for fitPLM() with one PM probesets and certain models
    Preliminary C code for 'quantile in blocks'
    Added normalize.quantiles.in.blocks()
    Changes in MAplot() to fit wiht the changes in ma.plot()
   
AnnBuilder
    Added GENENAME environment
   
annotate
    Removed revString(), now use reverseComplement() from Biostrings
   
beadarray
    Improved speed of findAllOutliers() by converting to C code
   
BeadExplorer
    New Package:
        QC, normalisation, annotation and exploration of Illumina BeadChip data
    Maintainer:
        Gareth Elvidge

Biobase
    Modified validity check on AssayData to ensure that rownames are consistent across members
    Added coercion from ExpressionSet to data.frame
    Added geneNames() and rowQ() for ExpressionSet; geneNames was added for compatibility and is marked deprecated
    rowQ(), rowMedians() are now methods for matrix, exprSet and ExpressionSet
    updateObjectFromSlots tries more aggressively to update objects
    Ensure that "[" for exprSet and eSet do not pretend to subset when mistakenly called with exprSet[name='something']
    Modified validity check on AssayData to ensure that rownames are consistent across members
   
biomaRt
    Fixed getGene() to work with all species in Ensembl
    Adapted getOMIM() as OMIM attribute is not present in current Ensembl release
    Removed martConnect() as now useMart() should now be used
   
BioMVCClass
    New Package:
        Creates classes used in model-view-controller (MVC) design
    Maintainer:
        Elizabeth Whalen

Biostrings
    Made changes to reverseComplement() to speed things up
    Added on-the-fly conversion to uppercase for DNAString() and RNAString()
    Improved man pages for reverseComplement() and alphabetFrequency()
    reverseComplement() now works on a BStringViews object
    Added as.list() method for BStringViews object, result is a list of BString objects (which is not the same as a BStringsObject)
    reverse() and reverseComplement() don't reverse the order of the views anymore
    Better error message issued by BString(), DNAString(), and RNAString()
    Implemented reverse(), complement() and reverseComplement() in C
   
BufferedMatrix
    Added colnames, rownames slots to BufferedMatrix object, and accessor and replacer methods for these
    Subsetting/indexing with these names is now supported
    Fixed problem when colMode is called on a matrix already in colMode
    Add R level access to ReadOnlyMode
    More effective use of the buffer in colSums, colMeans, colVars, colMin, colMax, Mean, Var, Max, Min

cellHTS
    writeReport() now exports everything to the topTable.txt file
   
copa
    Added S4 methods for input objects (matrix, exprSet, ExpressionSet)
    Fixed permutation p-value and fdr computation

EBImage
    Added vignette
    Added watershed function

gaggle
    Changed package from starting R goose (connecting to the gaggle boss) at .onLoad to separate function
    Allow gaggleInit to register with a boss on some other machine than 'localhost'
    Now warns against using a fully-qualified domain name when calling gaggleInit
   
genefilter
    Made rowttests an S4 generic
    Added methods for matrix, exprSet and ExpressionSet
   
GOstats
    Major revision to GOstats vignette
   
graph
    Fixed bug in removeNode() reported by Jonathan Swingon
    removeAttrDataItem() ignores requests to remove items that do not exist
    clearNodeData and clearEdgeData now use removeAttrDataItem which gives complete removal of attributes
   
Harshlight
    New Package:
        The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects)
        and a corrected AffyBatch object is returned. The defective areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection.
    Maintainer:
         Maurizio Pellegrino

iSNetwork
    Made all views interactive even if they aren't from the active MVC
    Fixed the creation of the model graph
    Added to the GUI for creating a GO graph child model
    Added heatmapNI(), which is a non-interactive heatmap function that allows multiple variables for row and column side images
    Now show gene symbold rather than affy ids on the heatmap plot
    Now it's possible to create a spreadsheet of the node attributes in a graph model
    Allowed users to show hidden values (rows, genes or nodes) through the GUI
    Changed the linking between genes and GO terms to take into account the many-to-many relationship
    Can now create a heatmap from a graph node
    Added methods and functions to create a gene set enrichment model and to create a qq-plot of that model
   
limma
    Bug fix to read.maimages: removed mention of readBlueFuseHeader which is no longer a function
    Edited man pages for RGList and MAList
    Improved normalizeQuantiles to reduce memory requirements
    decideTests now preserves row names
   
MLInterfaces
    Documented xval return values
    Changed xval to return feature selection structured to reflect cross-validations
   
multtest
    Fixed problem with strata in coxY()
   
MVCClass
    Moved some class definitions to BioMVCClass package to remove dependencies on Biobase, graph and Rgraphviz
    Added model variable slot to the model classes
    Added qqPlotView class for a qq plot of gene set enrichment data
   
oligo
    Added SnpQSet class
   
prada
    Added hist method for cytoFrames
    Gates of type polygon and rectangle can now be plotted as lines
    The function read.fsc() is a wrapper around readFCS() and read.FCS() from package rflowcyt and should standardize the different input functions for cytometry data
    Fixed bug in plotPlate()

prism
    New Package:
        This package can be used for gridding, segmentation and intensity estimation of cDNA microarray images.
        The method used is probabilistic and use Bayesian image analysis. The Expectation-Maximization (EM) combined to the Iterated Conditional Modes (ICM) algorithms
        or MCMC can be used to estimated the unknown parameters.
    Maintainer:
        Raphael Gottardo

quantsmooth
    New Package:
        Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.
    Maintainer:
        Jan Oosting

Rgraphviz
    Added ability to specify line type and width for graph edges, thanks to Mark Kimple for the patch
    Cosmetic changes to vignette
    Fixed bug in man page of image map
   
snapCGH
    Changed clustering method to 'clara' from 'pam', improving performance for large datasets

tilingArray
    Updated man page for plotAlongChrom to reflect new arguments
    Added man pages for plotAlongChromLegend, plotFeatures, plotSegmentationDots and plotSegmentationHeatmap
    Updated grid.image and plotAlongChrom to allow new along chromosome display options
    plotSegmentationDots and plotSegmentationHeatmap have new arguments and can operate as stand-alone functions
    plotAlongChromLegend is a function which can be called to create a separate legend for the genomic features (also called by plotAlongChrom when doLegend = TRUE
    Added a function for generating a text file of normalized probe intensities

vsn
    Removed nchoosek(), replaced with combn() from utils package