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Last data update: 2014.03.03

PSCBS

Package: PSCBS
Version: 0.61.0
Depends: R (>= 3.1.2), utils
Imports: R.methodsS3 (>= 1.7.0), R.oo (>= 1.19.0), R.utils (>= 2.2.0),
R.cache (>= 0.12.0), matrixStats (>= 0.50.1), DNAcopy (>=
1.40.0), listenv (>= 0.6.0), future (>= 0.11.0), parallel
Suggests: Hmisc (>= 3.16-0), R.rsp (>= 0.21.0), R.devices (>= 2.13.2),
ggplot2 (>= 1.0.1), aroma.light (>= 2.2.1)
SuggestsNote: BioC (>= 3.0), Recommended: Hmisc, aroma.light
VignetteBuilder: R.rsp
Date: 2016-02-03
Title: Analysis of Parent-Specific DNA Copy Numbers
Authors@R: c(
person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email="henrikb@braju.com"),
person("Pierre", "Neuvial", role="aut"),
person("Venkatraman E.", "Seshan", role="aut"),
person("Adam B.", "Olshen", role="aut"),
person("Paul T.", "Spellman", role="aut"),
person("Richard A.", "Olshen", role="aut"))
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
License: GPL (>= 2)
LazyLoad: TRUE
ByteCompile: TRUE
biocViews: aCGH, CopyNumberVariants, SNP, Microarray, OneChannel,
TwoChannel, Genetics
URL: https://github.com/HenrikBengtsson/PSCBS
BugReports: https://github.com/HenrikBengtsson/PSCBS/issues
NeedsCompilation: no
Packaged: 2016-02-04 00:30:07 UTC; hb
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Repository: CRAN
Date/Publication: 2016-02-04 11:27:36

● BiocViews: CopyNumberVariants, Genetics, Microarray, OneChannel, SNP, TwoChannel, aCGH
● 13 images, 85 functions, 0 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'PSCBS' ...
** package 'PSCBS' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PSCBS'
    finding HTML links ... done
    AbstractCBS                             html  
    CBS                                     html  
    Non-documented_objects                  html  
    NonPairedPSCBS                          html  
    PSCBS-package                           html  
    PSCBS                                   html  
    PairedPSCBS                             html  
    Restructuring_AbstractCBS_objects       html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/Restructuring_AbstractCBS_objects.Rd:24: missing file link 'extractChromosomes.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/Restructuring_AbstractCBS_objects.Rd:25: missing file link 'extractChromosome.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/Restructuring_AbstractCBS_objects.Rd:28: missing file link 'extractSegments.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/Restructuring_AbstractCBS_objects.Rd:29: missing file link 'extractSegment.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/Restructuring_AbstractCBS_objects.Rd:32: missing file link 'extractRegions.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/Restructuring_AbstractCBS_objects.Rd:33: missing file link 'extractRegion.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/Restructuring_AbstractCBS_objects.Rd:39: missing file link 'dropRegion.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/Restructuring_AbstractCBS_objects.Rd:43: missing file link 'dropChangePoint.AbstractCBS'
    append.AbstractCBS                      html  
    append.CBS                              html  
    append.PSCBS                            html  
    as.CBS.DNAcopy                          html  
    finding level-2 HTML links ... done

    as.DNAcopy.CBS                          html  
    as.data.frame.AbstractCBS               html  
    as.data.frame.CBS                       html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/as.data.frame.CBS.Rd:36: missing file link 'getSegments.CBS'
    bootstrapTCNandDHByRegion.PairedPSCBS   html  
    callAB.PairedPSCBS                      html  
    callAllelicBalanceByDH.PairedPSCBS      html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/callAllelicBalanceByDH.PairedPSCBS.Rd:53: missing file link 'callAllelicBalance.PairedPSCBS'
    callAmplifications.CBS                  html  
    callCopyNeutral.PairedPSCBS             html  
    callCopyNeutralByTCNofAB.PairedPSCBS    html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/callCopyNeutralByTCNofAB.PairedPSCBS.Rd:38: missing file link 'calcStatsForCopyNeutralABs.PairedPSCBS'
    callGNL.PairedPSCBS                     html  
    callGainsAndLosses.CBS                  html  
    callLOH.PairedPSCBS                     html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/callLOH.PairedPSCBS.Rd:62: missing file link 'callLowC1ByC1.PairedPSCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/callLOH.PairedPSCBS.Rd:63: missing file link 'callExtremeAllelicImbalanceByDH.PairedPSCBS'
    callOutliers.CBS                        html  
    callROH.PairedPSCBS                     html  
    callSegmentationOutliers                html  
    dropChangePoints.AbstractCBS            html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/dropChangePoints.AbstractCBS.Rd:18: missing file link 'dropChangePoint.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/dropChangePoints.AbstractCBS.Rd:31: missing file link 'dropChangePoint.AbstractCBS'
    dropRegions.AbstractCBS                 html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/dropRegions.AbstractCBS.Rd:34: missing file link 'extractRegions.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/dropRegions.AbstractCBS.Rd:50: missing file link 'extractRegions.AbstractCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/dropRegions.AbstractCBS.Rd:51: missing file link 'dropChangePoint.AbstractCBS'
    estimateDeltaAB.PairedPSCBS             html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/estimateDeltaAB.PairedPSCBS.Rd:45: missing file link 'estimateStdDevForHeterozygousBAF.PairedPSCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/estimateDeltaAB.PairedPSCBS.Rd:46: missing file link 'estimateMeanForDH.PairedPSCBS'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/estimateDeltaAB.PairedPSCBS.Rd:47: missing file link 'estimateHighDHQuantileAtAB.PairedPSCBS'
    estimateDeltaABBySmallDH.PairedPSCBS    html  
    estimateDeltaLOH.PairedPSCBS            html  
    estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS
                                            html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS.Rd:44: missing file link 'callAllelicBalance.PairedPSCBS'
    estimateKappa.PairedPSCBS               html  
    estimateKappaByC1Density.PairedPSCBS    html  
    estimateStandardDeviation.CBS           html  
    exampleData                             html  
    extractMinorMajorCNs.PairedPSCBS        html  
    extractSegmentMeansByLocus.CBS          html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/extractSegmentMeansByLocus.CBS.Rd:26: missing file link 'getLocusData.CBS'
    extractTCNAndDHs.PairedPSCBS            html  
    findLargeGaps                           html  
    findNeutralCopyNumberState              html  
    gapsToSegments.data.frame               html  
    getBootstrapLocusSets.PairedPSCBS       html  
    getCallStatistics.CBS                   html  
    getChromosomes.AbstractCBS              html  
    getFractionOfGenomeLost.CBS             html  
    getLocusData.AbstractCBS                html  
    getSampleName.AbstractCBS               html  
    getSegments.AbstractCBS                 html  
    getSegments.PSCBS                       html  
    getSmoothLocusData.CBS                  html  
    hclustCNs.AbstractCBS                   html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/hclustCNs.AbstractCBS.Rd:27: missing file link 'sampleCNs.AbstractCBS'
    installDNAcopy                          html  
    joinSegments.CBS                        html  
    load.AbstractCBS                        html  
    mergeNonCalledSegments.CBS              html  
    mergeThreeSegments.AbstractCBS          html  
    mergeTwoSegments.AbstractCBS            html  
    mergeTwoSegments.PairedPSCBS            html  
    nbrOfChangePoints.AbstractCBS           html  
    nbrOfChromosomes.AbstractCBS            html  
    nbrOfLoci.AbstractCBS                   html  
    nbrOfSegments.AbstractCBS               html  
    ploidy.AbstractCBS                      html  
    plotTracks.AbstractCBS                  html  
    plotTracks.CBS                          html  
    plotTracks.PairedPSCBS                  html  
    pruneByDP.AbstractCBS                   html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/pruneByDP.AbstractCBS.Rd:30: missing file link 'seqOfSegmentsByDP.AbstractCBS'
    pruneByHClust.AbstractCBS               html  
    pruneBySdUndo.CBS                       html  
    randomSeed                              html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/randomSeed.Rd:30: missing file link 'RNGkind'
    report.AbstractCBS                      html  
    resetSegments.AbstractCBS               html  
    save.AbstractCBS                        html  
    segmentByCBS                            html  
    segmentByNonPairedPSCBS                 html  
    segmentByPairedPSCBS                    html  
    setSampleName.AbstractCBS               html  
    testROH.numeric                         html  
    updateMeans.AbstractCBS                 html  
    updateMeansTogether.AbstractCBS         html  
    weightedQuantile                        html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/weightedQuantile.Rd:35: missing file link 'wtd.quantile'
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/weightedQuantile.Rd:50: missing file link 'wtd.quantile'
    writeSegments.CBS                       html  
Rd warning: /tmp/RtmpULNYku/R.INSTALL1df85072b061/PSCBS/man/writeSegments.CBS.Rd:48: missing file link 'getSegments.CBS'
    writeSegments.PSCBS                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PSCBS)
Making 'packages.html' ... done