November Changes in BioC Devel

    November 2005

aCGH
    Fixed a scaling issue with the xi variables. now the transition probability matrix always scales to one
    Added mergeLevels()
   
affxparser
    Added Fusion release 1
    Fixed type conversion bugs
   
affy
    Fixed y < alpha bug in mas5() and mas5calls()
    Modified parser so raw 'standard deviations' can be read in from celfiles
    Fixed double logging in MAplot() for paired samples
   
affycomp
    Added a namespace

affycoretools
    Removed unnecessary ylim argument from affystart()
    Changed API of probes2table
        -removed arguments tstat, pval, and FC
        -added argument otherdata, which is a *named* list
        -This allows addition of arbitrary data to HTML table instead of the three hardcoded choices
   
affyExonMuncher   
    New package:
        Package for Affymetrix exon array data annotation and visualization
   
    Maintainer:
        Jinhua Zhang

affyio
    New Package:
        Tools for parsing Affymetrix data files

    Maintainer:
        Benjamin Milo Bolstad

affyPLM
    Updated bg.correct.gcrma() so it wraps new bg.adjust.gcrma() function in gcrma package
   
   
AnnBuilder
    getGOBuilt modified to return the data when the XML file was last modified
    saveMat modified to remove leading and trailing spaces
    New environments for YEAST package
        -YEASTCOMMON2SYSTEMATIC
        -YEASTREJECTORF
        -YEASTPFAM
        -YEASTINTERPRO
    YEASTPFAM and YEASTINTERPRO use a new class YEAST-class
   
annotate
    Fixed function genbank() to work with current output from NCBI
    Added a namespace
    Removed isGeneric()
   
annotation packages
    New Features for BioConductor 1.7.0 Annotation Packages:

    a) New annotation packages
        1) For Affymetrix chips:
            - sugarcaneprobe
            - hu35ksuba, hu35ksubaprobe
            - hu35ksubb, hu35ksubbprobe
            - hu35ksubc, hu35ksubcprobe
            - hu35ksubd, hu35ksubdprobe
            - canine2, canine2cdf, canine2probe
            - medicagocdf, medicagoprobe
            - tomatocdf, tomatoprobe
        2) indac: for FlyChip_long_oligonucleotide_002 (FL002) chip
    b) New environments (*PFAM and *PROSITE) in human-, mouse-, and rat-chip
        annotation packages.  These two environments are created from
        the data in International Protein Index (IPI) website.  They
        provide the mappings between probe set ids and Pfam/PROSITE ids,
        respectively. 
    c) Modification of the DESCRIPTION files of annotation packages
        1) Add new fields:
            - organism
            - species
            - manufacturer
            - chipName
            - manufacturerUrl
            - biocViews
        2) Improve the "Title" and "Description" fields

arrayQuality
    arrayQuality now includes a new series of functions specifically
    designed for MEEBO arrays, which provide a wide range of control
    sequences, such as positive, negative, tiled and doping controls. The
    main function in producing quality plots for MEEBO arrays is called
    meeboQuality(); the results can be summarized in 3 categories:
   
    1- A figure including several statistics and exploratory plots. It is
    similar to the other diagnostic plots generated with other functions in
    this package and will provide a quick graphical insight on the quality
    of the array.
   
    2- QC on doping controls: these plots show the performance of the doping
    controls that were added to the hybridization mix, and compare them to
    expected results.
   
    3- Mismatch and tiled controls plots: these plots are designed to show
    the specificity of the MEEBO set and to examine the level of
    amplification bias toward the 3' end of the transcripts. These plots can
    be used as a MEEBO print-run QC rather than general hybridization
    quality assessment.

Biobase
    Added isUnique()
    Fixed documentation so individual functions stand out
   
Biostrings
    New vignette
    Added more fasta files
    Added namespace
    Removed isGeneric()
       
bridge
    Added a namespace

CoCiteStats
    Added a namespace
   
codelink
    New Package:
        Manipulation of Codelink Bioarrays Data.

    Maintainer:
        Diego Diez

     functions as well as the GUI.

DynDoc
    Added a namespace

EBImage
    New Package:
        imagine: R image processing toolkit
   
    Maintainer:
        Oleg Sklyar

edd
    Added a namespace

externalVector
    Added a namespace
    Removed isGeneric()
       
gcrma
    Added a namespace
   
geneArise
    The genArise package implement as a new feature in the GUI a swap analysis where
    a swap dye data file pair is the input. First, a flip dye consistency checking
    is performed using a 2 SD cut and removing spots with expression level
    inconsistency between this pair of swap dye replicates. Then a merged file is
    obtained where the merged intensities will be the geometric means of the swap
    dye replicates. After this you can perform the analysis as a single experiment.
GeneMeta
    Added a namespace
    Removed isGeneric()

GeneR
    Version 2
    New functions strWriteFasta() shuffleSeq(), randomSeq(), densityProfile(), bankDensityProfile(), GCcontent(), seqSkew(), deleteCR()
   
GOstats
    Added a namespace

hexbin
    Thanks to some help from Deepayan Sarkar, hexagon binning functions now
    work with grid. Implemented
    so far are hexbinplot (xyplot with hexbins) and hexplom (splom with
    hexbins). There are several panel functions
    for hexboxplots and other features. The group variable defaults to
    hexdiff plots.

    Also I am working on some added apply functions for hexbins to apply
    functions over margins of the hexagon
    grid and over hexagon neighborhoods. Finally, for spatial applications
    mainly, the ability to clip a hexgaon
    lattice by and arbitrary convex polygon.

Icens
    Added a namespace

ideogram
    Added a namespace

iSPlot
    Most importantly, the iSPlot package now works with its Namespace
    file.  The main addition to the iSPlot package has been adding
    command line functions to access the same functionality that is
    available through the GUI.  Thus, loading data, creating views and
    setting the response to interaction with views can all be done from
    the command line.  The vignette documents the new command line
KEGGSOAP
    Added a namespace

limma
    limma now formally depends on R >= 2.2.0
    cbind and rbind now support 'other' component in RGList and MAList objects
    Fixed decideTests() failing with method = "nestedF" and adjust.method = "BH"
    decideTests() now supports adjust.method = "BY"
    Clarification of help files to distinguish decideTests() and classifyTests()
    MAList subsetting now supports 'other' columns
    Bug fix to make sure makeContrasts() works correctly when level names are the same as local variable names
    Clarification of help files for lm.series(), gls.series() and mrlm() to indicate they are utility functions called by lmFit()
    Clarification of help file for lmFit() to better explain correlation argument
    Argument correlation in lmFit() no longer has a default value
    vennDiagram() example now uses decideTests() rather than classifyTestsF()
    fitFDist() now treats vary small and zero variances in a unified way
    This will slightly change hyperparameter estimates and significance results produced by eBayes()
    New option "rma" for method argument of backgroundCorrect()
    read.maimages() now uses check.names = FALSE to preserve annotation column names as input
    Examples for lmFit() expanded and those for helper functions (lm.series, gls.series, mlrm) removed
    intraspotCorrelation() output all.correlations renamed atanh.correlations
    duplicateCorrelation() now returns atanh.correlations
    read.maimages(source = "genepix") now uses X position column to determine printer layout information
    Bug fix - read.maimages(source = "genepix") was failing when there was only one block of spots
    Added section on Paired Samples to User's guide
    New S3 methods fitted() and residuals() for class MArrayLM
   
LPEP
    New Package:
        Local Pooled Error Test for Differential Expression with Paired High-throughput Data

    Maintainer:
        HyungJun Cho

makecdfenv
    Added a namespace
   
makePlatformDesign
    Reordered PDenv to make pm() and mm() faster
    Bugfix in readndf()
   
MANOR
    New label for unique.flag(); 'singlet' replaced by 'unique spot'
   
MCRestimate
    Fixed cluster.kmeans bug

metaArray
    New Package:
        Meta-Analysis of Microarray Data
   
    Maintainer:
        Hyungwon Choi

MVCClass
    Changed MVCClass to only contain class definitions and generic functions
    Added man pages for the classes
    Added a vignette
   
oligo
    Bugfix in readxys()
    Added i2xy() and xy2i()
    Changes in some methods to adapt to new ordering for PDenv

Prada
    Plot plate now accepts as optional argument a function producing grid
    graphics. This allows the user to plot arbitrary graphs in a plate array
    format. Also the function now uses the current graphic device for plotting.

PROcess
    Fixed the read.files() bug in win32 due to read.table/csv not handling gzfiles correctly
   

rama
    Added a namespace

Rdbi
    Added a namespace

RdbiPgSQL
    Added a namespace

reposTools
    Deprecated *.packages2 functions

rflowcyt
    Recent additions to rflowcyt include new visualization tools for
     data quality assessment of FCS objects (some already in BioC 1.7).
    Before the next release, we intend to add more plotting functions
    such as the plot plate function from the prada package (thanks to
    Florian Hahne).
   
    Also we are working on standardizing the outputs of the reading
    function of rflowcyt and prada.  I'm also creating some tests to
    run with RUnit.  Finally, we have added a namespace to the
    package.

Rgraphviz
    Fixed examples in the vignette
    Updated README to explain how to build more recent versions of graphviz and Rgraphviz
   
rhmetis
    Added arguments for node and hyperedge weights to allow weighted hypergraph partitioning
   
ROC
    Added a namespace

RSNPer
    Added a namespace

SAGElyzer
    Added a namespace

snapCGH
    New Package:
        Segmentation, normalisation and processing of aCGH data.
   
    Maintainer:
        Mike Smith

sscore
    New Package:
        S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
   
    Maintainer:
        Richard Kennedy

tilingArray
    moved antisense-UTR(), calcThreshold(), categorizeSegments(), readSegments() tableSegments() and writeSegmentTable() to davidTiling package
    uniqueInGenome() tries to estimate the amount of unique target sequence in the yeast genome
   
TypeInfo (formerly OptionalTyping)
    Added a method for hasParameterType generic for the class IndependentTypeSpecification
    Added documentation for the TypeSpecification classes
    Renamed OptionalTyping to TypeInfo