Package: PSCBS 0.67.0

PSCBS: Analysis of Parent-Specific DNA Copy Numbers

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.

Authors:Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut], Venkatraman E. Seshan [aut], Adam B. Olshen [aut], Paul T. Spellman [aut], Richard A. Olshen [aut], Frank E Harrell Jr [ctb]

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PSCBS/json (API)
NEWS

# Install 'PSCBS' in R:
install.packages('PSCBS', repos = c('https://henrikbengtsson.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/henrikbengtsson/pscbs/issues

On CRAN:

acghcopynumbervariantssnpmicroarrayonechanneltwochannelgenetics

7.59 score 7 stars 9 packages 34 scripts 768 downloads 6 mentions 437 exports 13 dependencies

Last updated 10 months agofrom:6860efd849 (on master). Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 13 2024
R-4.5-winNOTEDec 13 2024
R-4.5-linuxNOTEDec 13 2024
R-4.4-winOKDec 13 2024
R-4.4-macOKDec 13 2024
R-4.3-winOKDec 13 2024
R-4.3-macOKDec 13 2024

Exports:AbstractCBSadjustPloidyScaleadjustPloidyScale.AbstractCBSadjustPloidyScale.PairedPSCBSall.equal.AbstractCBSall.equal.CBSapplyByRegionapplyByRegion.PairedPSCBSarrowsC1C2arrowsC1C2.PairedPSCBSarrowsDeltaC1C2arrowsDeltaC1C2.PairedPSCBSas.CBSas.CBS.DNAcopyas.character.CBSas.data.frame.AbstractCBSas.data.frame.CBSas.data.frame.PSCBSas.DNAcopyas.DNAcopy.CBSbootstrapCIsbootstrapCIs.PairedPSCBSbootstrapSegmentsAndChangepointsbootstrapSegmentsAndChangepoints.PairedPSCBSbootstrapTCNandDHByRegionbootstrapTCNandDHByRegion.PairedPSCBSc.CBSc.PSCBScalcStatsForCopyNeutralABscalcStatsForCopyNeutralABs.PairedPSCBScallABcallAB.PairedPSCBScallABandHighAIcallABandHighAI.PairedPSCBScallABandLowC1callABandLowC1.PairedPSCBScallAllelicBalancecallAllelicBalance.defaultcallAllelicBalanceByDHcallAllelicBalanceByDH.PairedPSCBScallAmplificationscallAmplifications.CBScallArmscallArms.CBScallCopyNeutralcallCopyNeutral.PairedPSCBScallCopyNeutralByTCNofABcallCopyNeutralByTCNofAB.PairedPSCBScallExtremeAllelicImbalanceByDHcallExtremeAllelicImbalanceByDH.PairedPSCBScallGainNeutralLosscallGainNeutralLoss.PairedPSCBScallGainsAndLossescallGainsAndLosses.CBScallGLAOcallGLAO.CBScallGNLcallGNL.PairedPSCBScallGNLByTCNofABcallGNLByTCNofAB.PairedPSCBScallGNLByTCNofABv1callGNLByTCNofABv1.PairedPSCBScallLOHcallLOH.PairedPSCBScallLowC1ByC1callLowC1ByC1.PairedPSCBScallNTCNcallNTCN.PairedPSCBScallOutlierscallOutliers.CBScallROHcallROH.NonPairedPSCBScallROH.PairedPSCBScallROHOneSegmentcallROHOneSegment.PairedPSCBScallSegmentationOutlierscallSegmentationOutliers.data.framecallSegmentationOutliers.defaultCBSclearBootstrapSummariesclearBootstrapSummaries.PairedPSCBSclearCallsclearCalls.AbstractCBSdrawCentromeresdrawCentromeres.CBSdrawChangePointsdrawChangePoints.AbstractCBSdrawChangePoints.PSCBSdrawChangePointsC1C2drawChangePointsC1C2.PairedPSCBSdrawChromosomesdrawChromosomes.CBSdrawConfidenceBandsdrawConfidenceBands.PairedPSCBSdrawKnownSegmentsdrawKnownSegments.AbstractCBSdrawLevelsdrawLevels.CBSdrawLevels.DNAcopydrawLevels.PairedPSCBSdropChangePointdropChangePoint.AbstractCBSdropChangePointsdropChangePoints.AbstractCBSdropRegiondropRegion.AbstractCBSdropRegionsdropRegions.AbstractCBSdropSegmentationOutliersdropSegmentationOutliers.data.framedropSegmentationOutliers.defaultencodeCallsencodeCalls.data.frameestimateDeltaABestimateDeltaAB.PairedPSCBSestimateDeltaABBySmallDHestimateDeltaABBySmallDH.PairedPSCBSestimateDeltaCNestimateDeltaCN.CBSestimateDeltaCN.PairedPSCBSestimateDeltaLOHestimateDeltaLOH.PairedPSCBSestimateDeltaLOHByMinC1ForNonABestimateDeltaLOHByMinC1ForNonAB.PairedPSCBSestimateHighDHQuantileAtABestimateHighDHQuantileAtAB.PairedPSCBSestimateKappaestimateKappa.PairedPSCBSestimateKappaByC1DensityestimateKappaByC1Density.PairedPSCBSestimateMeanForDHestimateMeanForDH.PairedPSCBSestimateStandardDeviationestimateStandardDeviation.CBSestimateStandardDeviation.DNAcopyestimateStdDevForHeterozygousBAFestimateStdDevForHeterozygousBAF.PairedPSCBSexampleDataexampleData.defaultextractC1C2extractC1C2.PairedPSCBSextractCallsByLocusextractCallsByLocus.CBSextractCallsByLocus.PairedPSCBSextractChromosomeextractChromosome.AbstractCBSextractChromosomesextractChromosomes.AbstractCBSextractChromosomes.CBSextractChromosomes.PSCBSextractCNsextractCNs.AbstractCBSextractCNs.CBSextractCNs.PairedPSCBSextractDeltaC1C2extractDeltaC1C2.PairedPSCBSextractDhSegmentextractDhSegment.PairedPSCBSextractLocusLevelC1C2extractLocusLevelC1C2.PairedPSCBSextractLocusLevelTCNextractLocusLevelTCN.PairedPSCBSextractMinorMajorCNsextractMinorMajorCNs.PairedPSCBSextractRegionextractRegion.AbstractCBSextractRegionsextractRegions.AbstractCBSextractSegmentextractSegment.AbstractCBSextractSegmentDataByLocusextractSegmentDataByLocus.PairedPSCBSextractSegmentMeansByLocusextractSegmentMeansByLocus.CBSextractSegmentMeansByLocus.DNAcopyextractSegmentsextractSegments.AbstractCBSextractSegments.CBSextractSegments.PairedPSCBSextractTCNAndDHsextractTCNAndDHs.PairedPSCBSextractTotalCNsextractTotalCNs.CBSextractWIGextractWIG.AbstractCBSextractWIG.CBSextractWIG.PSCBSfindBootstrapSummariesfindBootstrapSummaries.PairedPSCBSfindLargeGapsfindLargeGaps.data.framefindLargeGaps.defaultfindNeutralCopyNumberStatefindNeutralCopyNumberState.defaultgapsToSegmentsgapsToSegments.data.framegetBootstrapLocusSetsgetBootstrapLocusSets.PairedPSCBSgetCallStatisticsgetCallStatistics.CBSgetCallStatisticsByArmsgetCallStatisticsByArms.CBSgetChangePointsgetChangePoints.AbstractCBSgetChangePoints.CBSgetChangePoints.PSCBSgetChromosomeOffsetsgetChromosomeOffsets.AbstractCBSgetChromosomeOffsets.PairedPSCBSgetChromosomeRangesgetChromosomeRanges.AbstractCBSgetChromosomeRanges.CBSgetChromosomeRanges.PairedPSCBSgetChromosomesgetChromosomes.AbstractCBSgetChromosomes.DNAcopygetFGAgetFGA.CBSgetFGGgetFGG.CBSgetFGLgetFGL.CBSgetFractionOfGenomeAlteredgetFractionOfGenomeAltered.CBSgetFractionOfGenomeGainedgetFractionOfGenomeGained.CBSgetFractionOfGenomeLostgetFractionOfGenomeLost.CBSgetLocusDatagetLocusData.AbstractCBSgetLocusData.CBSgetLocusData.NonPairedPSCBSgetLocusData.PairedPSCBSgetLocusData.PSCBSgetLocusSignalNamesgetLocusSignalNames.AbstractCBSgetLocusSignalNames.CBSgetLocusSignalNames.PSCBSgetMeanEstimatorsgetMeanEstimators.AbstractCBSgetSampleNamegetSampleName.AbstractCBSgetSampleNamesgetSampleNames.DNAcopygetSegmentsgetSegments.AbstractCBSgetSegments.CBSgetSegments.PSCBSgetSegmentSizesgetSegmentSizes.AbstractCBSgetSegmentTrackPrefixesgetSegmentTrackPrefixes.AbstractCBSgetSegmentTrackPrefixes.CBSgetSegmentTrackPrefixes.PSCBSgetSignalTypegetSignalType.CBSgetSmoothLocusDatagetSmoothLocusData.CBShasBootstrapSummarieshasBootstrapSummaries.PairedPSCBShclustCNshclustCNs.AbstractCBShighlightArmCallshighlightArmCalls.CBShighlightCallshighlightCalls.CBShighlightLocusCallshighlightLocusCalls.CBSinstallDNAcopyinstallDNAcopy.defaultisLocallyPhasedisLocallyPhased.PSCBSisSegmentSplitterisSegmentSplitter.CBSisSegmentSplitter.PSCBSisWholeChromosomeGainedisWholeChromosomeGained.CBSisWholeChromosomeLostisWholeChromosomeLost.CBSjoinSegmentsjoinSegments.CBSlinesC1C2linesC1C2.PairedPSCBSlinesDeltaC1C2linesDeltaC1C2.PairedPSCBSmergeNonCalledSegmentsmergeNonCalledSegments.CBSmergeThreeSegmentsmergeThreeSegments.AbstractCBSmergeTwoSegmentsmergeTwoSegments.AbstractCBSmergeTwoSegments.CBSmergeTwoSegments.PairedPSCBSnbrOfAmplificationsnbrOfAmplifications.CBSnbrOfChangePointsnbrOfChangePoints.AbstractCBSnbrOfChromosomesnbrOfChromosomes.AbstractCBSnbrOfGainsnbrOfGains.CBSnbrOfLocinbrOfLoci.AbstractCBSnbrOfLoci.DNAcopynbrOfLossesnbrOfLosses.CBSnbrOfSamplesnbrOfSamples.DNAcopynbrOfSegmentsnbrOfSegments.AbstractCBSnbrOfSegments.DNAcopyNonPairedPSCBSnormalizeTotalCNsnormalizeTotalCNs.AbstractCBSnormalizeTotalCNs.PSCBSPairedPSCBSploidyploidy.AbstractCBSploidy<-ploidy<-.AbstractCBSplot.CBSplot.PairedPSCBSplotC1C2plotC1C2.PairedPSCBSplotDeltaC1C2plotDeltaC1C2.PairedPSCBSplotTracksplotTracks.AbstractCBSplotTracks.CBSplotTracks.PairedPSCBSplotTracks1plotTracks1.PairedPSCBSplotTracks2plotTracks2.PairedPSCBSplotTracksManyChromosomesplotTracksManyChromosomes.CBSplotTracksManyChromosomes.PairedPSCBSpointsC1C2pointsC1C2.PairedPSCBSpointsDeltaC1C2pointsDeltaC1C2.PairedPSCBSpostsegmentTCNpostsegmentTCN.PairedPSCBSprint.AbstractCBSpruneByDPpruneByDP.AbstractCBSpruneByHClustpruneByHClust.AbstractCBSpruneBySdUndopruneBySdUndo.CBSPSCBSrandomSeedrenameChromosomesrenameChromosomes.AbstractCBSreportreport.AbstractCBSresegmentresegment.AbstractCBSresegment.CBSresegment.NonPairedPSCBSresegment.PairedPSCBSresetSegmentsresetSegments.AbstractCBSsampleCNssampleCNs.AbstractCBSsampleNamesampleName.AbstractCBSsampleName<-sampleName<-.AbstractCBSsegmentByCBSsegmentByCBS.CBSsegmentByCBS.CNAsegmentByCBS.data.framesegmentByCBS.defaultsegmentByNonPairedPSCBSsegmentByNonPairedPSCBS.data.framesegmentByNonPairedPSCBS.defaultsegmentByNonPairedPSCBS.PairedPSCBSsegmentByPairedPSCBSsegmentByPairedPSCBS.data.framesegmentByPairedPSCBS.defaultsegmentByPairedPSCBS.PairedPSCBSseqOfSegmentsByDPseqOfSegmentsByDP.AbstractCBSseqOfSegmentsByDP.CBSseqOfSegmentsByDP.matrixseqOfSegmentsByDP.PairedPSCBSsetLocusDatasetLocusData.AbstractCBSsetMeanEstimatorssetMeanEstimators.AbstractCBSsetPloidysetPloidy.AbstractCBSsetSampleNamesetSampleName.AbstractCBSsetSegmentssetSegments.AbstractCBSshiftTCNshiftTCN.AbstractCBSshiftTCN.CBSshiftTCN.PairedPSCBSsignalTypesignalType.CBSsignalType<-signalType<-.CBSsubset.CBStestROHtestROH.numerictileChromosomestileChromosomes.AbstractCBStileChromosomes.CBStileChromosomes.PairedPSCBSunTumorBoostunTumorBoost.PairedPSCBSupdateBoundariesupdateBoundaries.CBSupdateMeansupdateMeans.AbstractCBSupdateMeans.CBSupdateMeans.NonPairedPSCBSupdateMeans.PairedPSCBSupdateMeansC1C2updateMeansC1C2.PairedPSCBSupdateMeansTogetherupdateMeansTogether.AbstractCBSupdateMeansTogether.CBSupdateMeansTogether.PairedPSCBSweightedQuantileweightedQuantile.defaultwriteLocusDatawriteLocusData.CBSwriteSegmentswriteSegments.CBSwriteSegments.DNAcopywriteSegments.PSCBSwriteWIGwriteWIG.AbstractCBS

Dependencies:aroma.lightcodetoolsdigestDNAcopyfutureglobalslistenvmatrixStatsparallellyR.cacheR.methodsS3R.ooR.utils

Parent-specific copy-number segmentation using Paired PSCBS

Rendered fromPairedPSCBS.tex.rspusingR.rsp::rspon Dec 13 2024.

Last update: 2021-10-23
Started: 2013-10-14

Total copy-number segmentation using CBS

Rendered fromCBS.tex.rspusingR.rsp::rspon Dec 13 2024.

Last update: 2021-10-23
Started: 2013-10-14

Readme and manuals

Help Manual

Help pageTopics
Package PSCBSPSCBS-package
Calls/drops single-locus outliers along the genomecallSegmentationOutliers callSegmentationOutliers.data.frame callSegmentationOutliers.default dropSegmentationOutliers dropSegmentationOutliers.data.frame dropSegmentationOutliers.default
The CBS classCBS
Identifies gaps of a genome where there exist no observationsfindLargeGaps findLargeGaps.data.frame findLargeGaps.default
Gets the genomic segments that are complementary to the gapsgapsToSegments gapsToSegments.data.frame
The NonPairedPSCBS classNonPairedPSCBS
The PairedPSCBS classPairedPSCBS
The PSCBS classPSCBS
Segment genomic signals using the CBS methodsegmentByCBS segmentByCBS.CBS segmentByCBS.CNA segmentByCBS.data.frame segmentByCBS.default
Segment total copy numbers and allele B fractions using the Non-paired PSCBS methodsegmentByNonPairedPSCBS segmentByNonPairedPSCBS.data.frame segmentByNonPairedPSCBS.default segmentByNonPairedPSCBS.PairedPSCBS
Segment total copy numbers and allele B fractions using the Paired PSCBS methodsegmentByPairedPSCBS segmentByPairedPSCBS.data.frame segmentByPairedPSCBS.default segmentByPairedPSCBS.PairedPSCBS