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.

Install the latest version of this package by entering the following in R:
install.packages("PSCBS")
AuthorHenrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut], Venkatraman E. Seshan [aut], Adam B. Olshen [aut], Paul T. Spellman [aut], Richard A. Olshen [aut]
Bioconductor views CopyNumberVariants Genetics Microarray OneChannel SNP TwoChannel aCGH
Date of publication2016-11-11 00:23:02
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseGPL (>= 2)
Version0.62.0
https://github.com/HenrikBengtsson/PSCBS

View on CRAN

Man pages

AbstractCBS: The AbstractCBS class

append.AbstractCBS: Appends one segmentation result to another

append.CBS: Appends one segmentation result to another

append.PSCBS: Appends one segmentation result to another

as.CBS.DNAcopy: Coerces a DNAcopy object to a CBS object

as.data.frame.AbstractCBS: Gets the table of segments

as.data.frame.CBS: Gets the table of segments

as.DNAcopy.CBS: Coerces a CBS object to a DNAcopy object

bootstrapTCNandDHByRegion.PairedPSCBS: Estimate confidence intervals of TCN and DH segment levels

callAB.PairedPSCBS: Calls segments that are in allelic balance

callAllelicBalanceByDH.PairedPSCBS: Calls segments that are in allelic balance

callAmplifications.CBS: Calls (focal) amplifications

callCopyNeutralByTCNofAB.PairedPSCBS: Calls regions that are copy neutral

callCopyNeutral.PairedPSCBS: Calls segments that have a neutral total copy number

callGainsAndLosses.CBS: Calls gains and losses

callGNL.PairedPSCBS: Calls segments that are gained, copy neutral, or lost

callLOH.PairedPSCBS: Calls segments that are in LOH

callOutliers.CBS: Calls outliers

callROH.PairedPSCBS: Calls segments that are in ROH

callSegmentationOutliers: Calls/drops single-locus outliers along the genome

CBS: The CBS class

dropChangePoints.AbstractCBS: Drops zero or more change points

dropRegions.AbstractCBS: Drops chromosomal regions (a connected set of segments)

estimateDeltaABBySmallDH.PairedPSCBS: Estimate a threshold for calling allelic balance from DH

estimateDeltaAB.PairedPSCBS: Estimate a threshold for calling allelic balance from DH

estimateDeltaCN.PairedPSCBS: Estimates the length of one total copy-number (TCN) unit

estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS: Estimate a threshold for calling LOH from DH

estimateDeltaLOH.PairedPSCBS: Estimate a threshold for calling LOH from DH

estimateKappaByC1Density.PairedPSCBS: Estimate global background in segmented copy numbers

estimateKappa.PairedPSCBS: Estimate global background in segmented copy numbers

estimateStandardDeviation.CBS: Estimates the whole-genome standard deviation of the signals

exampleData: Gets an example data set

extractMinorMajorCNs.PairedPSCBS: Extract minor and major copy-number mean levels per segment

extractSegmentMeansByLocus.CBS: Extracts segments means at each locus

extractTCNAndDHs.PairedPSCBS: Extract TCN and DH mean levels per segment

findLargeGaps: Identifies gaps of a genome where there exist no observations

findNeutralCopyNumberState: Call segments to be copy neutral based on allelic imbalance...

gapsToSegments.data.frame: Gets the genomic segments that are complementary to the gaps

getBootstrapLocusSets.PairedPSCBS: Generates original and bootstrapped segment-specific index...

getCallStatistics.CBS: Calculates various call statistics per chromosome

getChromosomes.AbstractCBS: Gets the set of chromosomes

getFractionOfGenomeLost.CBS: Calculates the fraction of the genome lost, gained, or...

getLocusData.AbstractCBS: Gets the locus-level data

getSampleName.AbstractCBS: Gets the name of the sample segmented

getSegments.AbstractCBS: Gets the segments

getSegments.PSCBS: Gets the segments

getSmoothLocusData.CBS: Gets smoothed locus-level data

hclustCNs.AbstractCBS: Performs a hierarchical clustering of the CN mean levels

installDNAcopy: Install the DNAcopy package

joinSegments.CBS: Joins neighboring segments such that there is no gap in...

load.AbstractCBS: Loads an AbstractCBS object from file

mergeNonCalledSegments.CBS: Merge neighboring segments that are not called

mergeThreeSegments.AbstractCBS: Merge a segment and its two flanking segments

mergeTwoSegments.AbstractCBS: Merge two neighboring segments

mergeTwoSegments.PairedPSCBS: Merge two neighboring segments

nbrOfChangePoints.AbstractCBS: Gets the number of change points

nbrOfChromosomes.AbstractCBS: Gets the number of chromosomes

nbrOfLoci.AbstractCBS: Gets the number of loci

nbrOfSegments.AbstractCBS: Gets the number of segments

Non-documented_objects: Non-documented objects

NonPairedPSCBS: The NonPairedPSCBS class

normalizeTotalCNs.AbstractCBS: Normalizes copy numbers such that the whole-genome average...

PairedPSCBS: The PairedPSCBS class

ploidy.AbstractCBS: Gets and sets ploidy

plotTracks.AbstractCBS: Plots the segmentation result along the genome

plotTracks.CBS: Plots copy numbers along the genome

plotTracks.PairedPSCBS: Plots parental specific copy numbers along the genome

pruneByDP.AbstractCBS: Prunes the CN profile using dynamical programming

pruneByHClust.AbstractCBS: Prunes the CN profile by pruning and merging through...

pruneBySdUndo.CBS: Prune the CBS profile by dropping change points that are too...

PSCBS: The PSCBS class

PSCBS-package: Package PSCBS

randomSeed: Sets and resets the .Random.seed in the global environment

report.AbstractCBS: Generates a report of the segmentation results

resetSegments.AbstractCBS: Reset the segments

Restructuring_AbstractCBS_objects: Restructuring AbstractCBS objects

save.AbstractCBS: Saves an AbstractCBS object to file

segmentByCBS: Segment genomic signals using the CBS method

segmentByNonPairedPSCBS: Segment total copy numbers and allele B fractions using the...

segmentByPairedPSCBS: Segment total copy numbers and allele B fractions using the...

setSampleName.AbstractCBS: Sets the name of the sample segmented

testROH.numeric: Tests if a segment is in Run-of-Homozygosity (ROH)

updateMeans.AbstractCBS: Updates the CN mean levels for each segment independently

updateMeansTogether.AbstractCBS: Updates the CN mean levels jointly in sets of segments

weightedQuantile: Weighted Quantile Value

writeSegments.CBS: Writes the table of segments to file

writeSegments.PSCBS: Writes the table of segments to file

Functions

AbstractCBS Man page
AbstractCBS.adjustPloidyScale Man page
AbstractCBS.append Man page
AbstractCBS.as.data.frame Man page
AbstractCBS.dropChangePoint Man page
AbstractCBS.dropChangePoints Man page
AbstractCBS.dropRegion Man page
AbstractCBS.dropRegions Man page
AbstractCBS.getChromosomes Man page
AbstractCBS.getLocusData Man page
AbstractCBS.getSampleName Man page
AbstractCBS.getSegments Man page
AbstractCBS.hclustCNs Man page
AbstractCBS.load Man page
AbstractCBS$load Man page
AbstractCBS.mergeThreeSegments Man page
AbstractCBS.mergeTwoSegments Man page
AbstractCBS.nbrOfChangePoints Man page
AbstractCBS.nbrOfChromosomes Man page
AbstractCBS.nbrOfLoci Man page
AbstractCBS.nbrOfSegments Man page
AbstractCBS.normalizeTotalCNs Man page
AbstractCBS.ploidy Man page
AbstractCBS.ploidy<- Man page
AbstractCBS.plotTracks Man page
AbstractCBS.pruneByDP Man page
AbstractCBS.pruneByHClust Man page
AbstractCBS.report Man page
AbstractCBS.resetSegments Man page
AbstractCBS.sampleName Man page
AbstractCBS.sampleName<- Man page
AbstractCBS.save Man page
AbstractCBS.setLocusData Man page
AbstractCBS.setPloidy Man page
AbstractCBS.setSampleName Man page
AbstractCBS.setSegments Man page
AbstractCBS.updateMeans Man page
AbstractCBS.updateMeansTogether Man page
adjustPloidyScale Man page
adjustPloidyScale.AbstractCBS Man page
adjustPloidyScale,AbstractCBS-method Man page
adjustPloidyScale.PairedPSCBS Man page
all.equal.AbstractCBS Man page
all.equal.CBS Man page
append Man page
append.AbstractCBS Man page
append,AbstractCBS-method Man page
append.CBS Man page
append,CBS-method Man page
append.default Man page
append.PSCBS Man page
append,PSCBS-method Man page
applyByRegion Man page
applyByRegion.PairedPSCBS Man page
arrowsC1C2 Man page
arrowsC1C2.PairedPSCBS Man page
arrowsDeltaC1C2 Man page
arrowsDeltaC1C2.PairedPSCBS Man page
as.CBS Man page
as.CBS.DNAcopy Man page
as.CBS,DNAcopy-method Man page
as.character.CBS Man page
as.data.frame.AbstractCBS Man page
as.data.frame,AbstractCBS-method Man page
as.data.frame.CBS Man page
as.data.frame,CBS-method Man page
as.data.frame.PSCBS Man page
as.DNAcopy Man page
as.DNAcopy.CBS Man page
as.DNAcopy,CBS-method Man page
bootstrapCIs Man page
bootstrapCIs.PairedPSCBS Man page
bootstrapDHByRegion Man page
bootstrapDHByRegion.PairedPSCBS Man page
bootstrapSegmentsAndChangepoints Man page
bootstrapSegmentsAndChangepoints.PairedPSCBS Man page
bootstrapTCNandDHByRegion Man page
bootstrapTCNandDHByRegion.PairedPSCBS Man page
bootstrapTCNandDHByRegion,PairedPSCBS-method Man page
calcStatsForCopyNeutralABs Man page
calcStatsForCopyNeutralABs.PairedPSCBS Man page
callAB Man page
callABandHighAI Man page
callABandHighAI.PairedPSCBS Man page
callABandLowC1 Man page
callABandLowC1.PairedPSCBS Man page
callAB.PairedPSCBS Man page
callAB,PairedPSCBS-method Man page
callAllelicBalance Man page
callAllelicBalanceByDH Man page
callAllelicBalanceByDH.PairedPSCBS Man page
callAllelicBalanceByDH,PairedPSCBS-method Man page
callAllelicBalance.default Man page
callAllelicBalance.PairedPSCBS Man page
callAllelicBalance,PairedPSCBS-method Man page
callAmplifications Man page
callAmplifications.CBS Man page
callAmplifications,CBS-method Man page
callArms Man page
callArms.CBS Man page
callCopyNeutral Man page
callCopyNeutralByTCNofAB Man page
callCopyNeutralByTCNofAB.PairedPSCBS Man page
callCopyNeutralByTCNofAB,PairedPSCBS-method Man page
callCopyNeutral.PairedPSCBS Man page
callCopyNeutral,PairedPSCBS-method Man page
callExtremeAllelicImbalanceByDH Man page
callExtremeAllelicImbalanceByDH.PairedPSCBS Man page
callGainNeutralLoss Man page
callGainNeutralLoss.PairedPSCBS Man page
callGainNeutralLoss,PairedPSCBS-method Man page
callGainsAndLosses Man page
callGainsAndLosses.CBS Man page
callGainsAndLosses,CBS-method Man page
callGLAO Man page
callGLAO.CBS Man page
callGNL Man page
callGNLByTCNofAB Man page
callGNLByTCNofAB.PairedPSCBS Man page
callGNLByTCNofAB,PairedPSCBS-method Man page
callGNLByTCNofABv1 Man page
callGNLByTCNofABv1.PairedPSCBS Man page
callGNLByTCNofABv1,PairedPSCBS-method Man page
callGNL.PairedPSCBS Man page
callGNL,PairedPSCBS-method Man page
callLOH Man page
callLOH.PairedPSCBS Man page
callLOH,PairedPSCBS-method Man page
callLowC1ByC1 Man page
callLowC1ByC1.PairedPSCBS Man page
callNTCN Man page
callNTCN.PairedPSCBS Man page
callNTCN,PairedPSCBS-method Man page
callOutliers Man page
callOutliers.CBS Man page
callOutliers,CBS-method Man page
callROH Man page
callROH.NonPairedPSCBS Man page
callROHOneSegment Man page
callROHOneSegment.PairedPSCBS Man page
callROH.PairedPSCBS Man page
callROH,PairedPSCBS-method Man page
callSegmentationOutliers Man page
callSegmentationOutliers.data.frame Man page
callSegmentationOutliers.default Man page
CBS Man page
CBS.append Man page
CBS.as.data.frame Man page
CBS.as.DNAcopy Man page
CBS.callAmplifications Man page
CBS.callGainsAndLosses Man page
CBS.callOutliers Man page
CBS.estimateStandardDeviation Man page
CBS.extractSegmentMeansByLocus Man page
CBS.getCallStatistics Man page
CBS.getFGA Man page
CBS.getFGG Man page
CBS.getFGL Man page
CBS.getFractionOfGenomeAltered Man page
CBS.getFractionOfGenomeGained Man page
CBS.getFractionOfGenomeLost Man page
CBS.getSmoothLocusData Man page
CBS.joinSegments Man page
CBS.mergeNonCalledSegments Man page
CBS.plotTracks Man page
CBS.pruneBySdUndo Man page
CBS.writeSegments Man page
clearBootstrapSummaries Man page
clearBootstrapSummaries.PairedPSCBS Man page
clearCalls Man page
clearCalls.AbstractCBS Man page
DNAcopy.as.CBS Man page
drawCentromeres Man page
drawCentromeres.CBS Man page
drawChangePoints Man page
drawChangePoints.AbstractCBS Man page
drawChangePointsC1C2 Man page
drawChangePointsC1C2.PairedPSCBS Man page
drawChangePoints.CBS Man page
drawChangePoints.PSCBS Man page
drawChromosomes Man page
drawChromosomes.CBS Man page
drawConfidenceBands Man page
drawConfidenceBands.PairedPSCBS Man page
drawKnownSegments Man page
drawKnownSegments.AbstractCBS Man page
drawLevels Man page
drawLevels.CBS Man page
drawLevels.DNAcopy Man page
drawLevels.PairedPSCBS Man page
dropChangePoint Man page
dropChangePoint.AbstractCBS Man page
dropChangePoint,AbstractCBS-method Man page
dropChangePoints Man page
dropChangePoints.AbstractCBS Man page
dropChangePoints,AbstractCBS-method Man page
dropRegion Man page
dropRegion.AbstractCBS Man page
dropRegion,AbstractCBS-method Man page
dropRegions Man page
dropRegions.AbstractCBS Man page
dropRegions,AbstractCBS-method Man page
dropSegmentationOutliers Man page
dropSegmentationOutliers.data.frame Man page
dropSegmentationOutliers.default Man page
encodeCalls Man page
encodeCalls.data.frame Man page
estimateDeltaAB Man page
estimateDeltaABBySmallDH Man page
estimateDeltaABBySmallDH.PairedPSCBS Man page
estimateDeltaABBySmallDH,PairedPSCBS-method Man page
estimateDeltaAB.PairedPSCBS Man page
estimateDeltaAB,PairedPSCBS-method Man page
estimateDeltaCN Man page
estimateDeltaCN.CBS Man page
estimateDeltaCN.PairedPSCBS Man page
estimateDeltaCN,PairedPSCBS-method Man page
estimateDeltaLOH Man page
estimateDeltaLOHByMinC1ForNonAB Man page
estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS Man page
estimateDeltaLOHByMinC1ForNonAB,PairedPSCBS-method Man page
estimateDeltaLOH.PairedPSCBS Man page
estimateDeltaLOH,PairedPSCBS-method Man page
estimateHighDHQuantileAtAB Man page
estimateHighDHQuantileAtAB.PairedPSCBS Man page
estimateKappa Man page
estimateKappaByC1Density Man page
estimateKappaByC1Density.PairedPSCBS Man page
estimateKappaByC1Density,PairedPSCBS-method Man page
estimateKappa.PairedPSCBS Man page
estimateKappa,PairedPSCBS-method Man page
estimateMeanForDH Man page
estimateMeanForDH.PairedPSCBS Man page
estimateStandardDeviation Man page
estimateStandardDeviation.CBS Man page
estimateStandardDeviation,CBS-method Man page
estimateStandardDeviation.DNAcopy Man page
estimateStdDevForHeterozygousBAF Man page
estimateStdDevForHeterozygousBAF.PairedPSCBS Man page
exampleData Man page
exampleData.default Man page
extractC1C2 Man page
extractC1C2.PairedPSCBS Man page
extractC1C2,PairedPSCBS-method Man page
extractCallsByLocus Man page
extractCallsByLocus.CBS Man page
extractCallsByLocus.PairedPSCBS Man page
extractChromosome Man page
extractChromosome.AbstractCBS Man page
extractChromosomes Man page
extractChromosomes.AbstractCBS Man page
extractChromosomes.CBS Man page
extractChromosomes.PSCBS Man page
extractCNs Man page
extractCNs.AbstractCBS Man page
extractCNs.CBS Man page
extractCNs.PairedPSCBS Man page
extractDeltaC1C2 Man page
extractDeltaC1C2.PairedPSCBS Man page
extractDhSegment Man page
extractDhSegment.PairedPSCBS Man page
extractLocusLevelC1C2 Man page
extractLocusLevelC1C2.PairedPSCBS Man page
extractLocusLevelTCN Man page
extractLocusLevelTCN.PairedPSCBS Man page
extractMinorMajorCNs Man page
extractMinorMajorCNs.PairedPSCBS Man page
extractMinorMajorCNs,PairedPSCBS-method Man page
extractRegion Man page
extractRegion.AbstractCBS Man page
extractRegions Man page
extractRegions.AbstractCBS Man page
extractSegment Man page
extractSegment.AbstractCBS Man page
extractSegmentDataByLocus Man page
extractSegmentDataByLocus.PairedPSCBS Man page
extractSegmentMeansByLocus Man page
extractSegmentMeansByLocus.CBS Man page
extractSegmentMeansByLocus,CBS-method Man page
extractSegmentMeansByLocus.DNAcopy Man page
extractSegments Man page
extractSegments.AbstractCBS Man page
extractSegments.CBS Man page
extractSegments.PairedPSCBS Man page
extractTCNAndDHs Man page
extractTCNAndDHs.PairedPSCBS Man page
extractTCNAndDHs,PairedPSCBS-method Man page
extractTotalCNs Man page
extractTotalCNs.CBS Man page
extractWIG Man page
extractWIG.AbstractCBS Man page
extractWIG.CBS Man page
extractWIG.PSCBS Man page
findBootstrapSummaries Man page
findBootstrapSummaries.PairedPSCBS Man page
findLargeGaps Man page
findLargeGaps.data.frame Man page
findLargeGaps.default Man page
findNeutralCopyNumberState Man page
findNeutralCopyNumberState.default Man page
gapsToSegments Man page
gapsToSegments.data.frame Man page
getBootstrapLocusSets Man page
getBootstrapLocusSets.PairedPSCBS Man page
getBootstrapLocusSets,PairedPSCBS-method Man page
getCallStatistics Man page
getCallStatisticsByArms Man page
getCallStatisticsByArms.CBS Man page
getCallStatistics.CBS Man page
getCallStatistics,CBS-method Man page
getChangePoints Man page
getChangePoints.AbstractCBS Man page
getChangePoints.CBS Man page
getChangePoints.PSCBS Man page
getChromosomeOffsets Man page
getChromosomeOffsets.AbstractCBS Man page
getChromosomeOffsets.PairedPSCBS Man page
getChromosomeRanges Man page
getChromosomeRanges.AbstractCBS Man page
getChromosomeRanges.CBS Man page
getChromosomeRanges.PairedPSCBS Man page
getChromosomes Man page
getChromosomes.AbstractCBS Man page
getChromosomes,AbstractCBS-method Man page
getChromosomes.DNAcopy Man page
getFGA Man page
getFGA.CBS Man page
getFGA,CBS-method Man page
getFGG Man page
getFGG.CBS Man page
getFGG,CBS-method Man page
getFGL Man page
getFGL.CBS Man page
getFGL,CBS-method Man page
getFractionOfGenomeAltered Man page
getFractionOfGenomeAltered.CBS Man page
getFractionOfGenomeAltered,CBS-method Man page
getFractionOfGenomeGained Man page
getFractionOfGenomeGained.CBS Man page
getFractionOfGenomeGained,CBS-method Man page
getFractionOfGenomeLost Man page
getFractionOfGenomeLost.CBS Man page
getFractionOfGenomeLost,CBS-method Man page
getLocusData Man page
getLocusData.AbstractCBS Man page
getLocusData,AbstractCBS-method Man page
getLocusData.CBS Man page
getLocusData.NonPairedPSCBS Man page
getLocusData.PairedPSCBS Man page
getLocusData.PSCBS Man page
getLocusSignalNames Man page
getLocusSignalNames.AbstractCBS Man page
getLocusSignalNames.CBS Man page
getLocusSignalNames.PSCBS Man page
getMeanEstimators Man page
getMeanEstimators.AbstractCBS Man page
getSampleName Man page
getSampleName.AbstractCBS Man page
getSampleName,AbstractCBS-method Man page
getSampleNames Man page
getSampleNames.DNAcopy Man page
getSegments Man page
getSegments.AbstractCBS Man page
getSegments,AbstractCBS-method Man page
getSegments.CBS Man page
getSegmentSizes Man page
getSegmentSizes.AbstractCBS Man page
getSegmentSizes.CBS Man page
getSegmentSizes.PSCBS Man page
getSegments.PSCBS Man page
getSegments,PSCBS-method Man page
getSegmentTrackPrefixes Man page
getSegmentTrackPrefixes.AbstractCBS Man page
getSegmentTrackPrefixes.CBS Man page
getSegmentTrackPrefixes.PSCBS Man page
getSignalType Man page
getSignalType.CBS Man page
getSmoothLocusData Man page
getSmoothLocusData.CBS Man page
getSmoothLocusData,CBS-method Man page
hasBootstrapSummaries Man page
hasBootstrapSummaries.PairedPSCBS Man page
hclustCNs Man page
hclustCNs.AbstractCBS Man page
hclustCNs,AbstractCBS-method Man page
highlightArmCalls Man page
highlightArmCalls.CBS Man page
highlightCalls Man page
highlightCalls.CBS Man page
highlightLocusCalls Man page
highlightLocusCalls.CBS Man page
installDNAcopy Man page
installDNAcopy.default Man page
isSegmentSplitter Man page
isSegmentSplitter.CBS Man page
isSegmentSplitter.PSCBS Man page
isWholeChromosomeGained Man page
isWholeChromosomeGained.CBS Man page
isWholeChromosomeLost Man page
isWholeChromosomeLost.CBS Man page
joinSegments Man page
joinSegments.CBS Man page
joinSegments,CBS-method Man page
linesC1C2 Man page
linesC1C2.PairedPSCBS Man page
linesDeltaC1C2 Man page
linesDeltaC1C2.PairedPSCBS Man page
load Man page
load.AbstractCBS Man page
load,AbstractCBS-method Man page
mergeNonCalledSegments Man page
mergeNonCalledSegments.CBS Man page
mergeNonCalledSegments,CBS-method Man page
mergeThreeSegments Man page
mergeThreeSegments.AbstractCBS Man page
mergeThreeSegments,AbstractCBS-method Man page
mergeTwoSegments Man page
mergeTwoSegments.AbstractCBS Man page
mergeTwoSegments,AbstractCBS-method Man page
mergeTwoSegments.CBS Man page
mergeTwoSegments.PairedPSCBS Man page
mergeTwoSegments,PairedPSCBS-method Man page
nbrOfAmplifications Man page
nbrOfAmplifications.CBS Man page
nbrOfChangePoints Man page
nbrOfChangePoints.AbstractCBS Man page
nbrOfChangePoints,AbstractCBS-method Man page
nbrOfChromosomes Man page
nbrOfChromosomes.AbstractCBS Man page
nbrOfChromosomes,AbstractCBS-method Man page
nbrOfGains Man page
nbrOfGains.CBS Man page
nbrOfLoci Man page
nbrOfLoci.AbstractCBS Man page
nbrOfLoci,AbstractCBS-method Man page
nbrOfLoci.DNAcopy Man page
nbrOfLosses Man page
nbrOfLosses.CBS Man page
nbrOfSamples Man page
nbrOfSamples.DNAcopy Man page
nbrOfSegments Man page
nbrOfSegments.AbstractCBS Man page
nbrOfSegments,AbstractCBS-method Man page
nbrOfSegments.DNAcopy Man page
Non-documented objects Man page
NonPairedPSCBS Man page
normalizeTotalCNs Man page
normalizeTotalCNs.AbstractCBS Man page
normalizeTotalCNs,AbstractCBS-method Man page
normalizeTotalCNs.PSCBS Man page
PairedPSCBS Man page
PairedPSCBS.bootstrapTCNandDHByRegion Man page
PairedPSCBS.callAB Man page
PairedPSCBS.callAllelicBalance Man page
PairedPSCBS.callAllelicBalanceByDH Man page
PairedPSCBS.callCopyNeutral Man page
PairedPSCBS.callCopyNeutralByTCNofAB Man page
PairedPSCBS.callGainNeutralLoss Man page
PairedPSCBS.callGNL Man page
PairedPSCBS.callGNLByTCNofAB Man page
PairedPSCBS.callGNLByTCNofABv1 Man page
PairedPSCBS.callLOH Man page
PairedPSCBS.callNTCN Man page
PairedPSCBS.callROH Man page
PairedPSCBS.estimateDeltaAB Man page
PairedPSCBS.estimateDeltaABBySmallDH Man page
PairedPSCBS.estimateDeltaCN Man page
PairedPSCBS.estimateDeltaLOH Man page
PairedPSCBS.estimateDeltaLOHByMinC1ForNonAB Man page
PairedPSCBS.estimateKappa Man page
PairedPSCBS.estimateKappaByC1Density Man page
PairedPSCBS.extractC1C2 Man page
PairedPSCBS.extractMinorMajorCNs Man page
PairedPSCBS.extractTCNAndDHs Man page
PairedPSCBS.getBootstrapLocusSets Man page
PairedPSCBS.mergeTwoSegments Man page
PairedPSCBS.plotTracks Man page
PairedPSCBS.plotTracks1 Man page
PairedPSCBS.plotTracks2 Man page
PairedPSCBS.plotTracksManyChromosomes Man page
ploidy Man page
ploidy<- Man page
ploidy<-.AbstractCBS Man page
ploidy.AbstractCBS Man page
ploidy<-,AbstractCBS-method Man page
ploidy,AbstractCBS-method Man page
plot Man page
plotC1C2 Man page
plotC1C2.PairedPSCBS Man page
plot.CBS Man page
plotDeltaC1C2 Man page
plotDeltaC1C2.PairedPSCBS Man page
plot.PairedPSCBS Man page
plotTracks Man page
plotTracks1 Man page
plotTracks1.PairedPSCBS Man page
plotTracks1,PairedPSCBS-method Man page
plotTracks2 Man page
plotTracks2.PairedPSCBS Man page
plotTracks2,PairedPSCBS-method Man page
plotTracks.AbstractCBS Man page
plotTracks,AbstractCBS-method Man page
plotTracks.CBS Man page
plotTracks,CBS-method Man page
plotTracksManyChromosomes Man page
plotTracksManyChromosomes.CBS Man page
plotTracksManyChromosomes.PairedPSCBS Man page
plotTracksManyChromosomes,PairedPSCBS-method Man page
plotTracks.PairedPSCBS Man page
plotTracks,PairedPSCBS-method Man page
pointsC1C2 Man page
pointsC1C2.PairedPSCBS Man page
pointsDeltaC1C2 Man page
pointsDeltaC1C2.PairedPSCBS Man page
postsegmentTCN Man page
postsegmentTCN.PairedPSCBS Man page
print.AbstractCBS Man page
pruneByDP Man page
pruneByDP.AbstractCBS Man page
pruneByDP,AbstractCBS-method Man page
pruneByHClust Man page
pruneByHClust.AbstractCBS Man page
pruneByHClust,AbstractCBS-method Man page
pruneBySdUndo Man page
pruneBySdUndo.CBS Man page
pruneBySdUndo,CBS-method Man page
PSCBS Man page
PSCBS.append Man page
PSCBS.getSegments Man page
PSCBS-package Man page
PSCBS.writeSegments Man page
randomSeed Man page
renameChromosomes Man page
renameChromosomes.AbstractCBS Man page
report Man page
report.AbstractCBS Man page
report,AbstractCBS-method Man page
resegment Man page
resegment.AbstractCBS Man page
resegment.CBS Man page
resegment.NonPairedPSCBS Man page
resegment.PairedPSCBS Man page
resetSegments Man page
resetSegments.AbstractCBS Man page
resetSegments,AbstractCBS-method Man page
RestructPSCBS Man page
Restructuring AbstractCBS objects Man page
sampleCNs Man page
sampleCNs.AbstractCBS Man page
sampleName Man page
sampleName<- Man page
sampleName<-.AbstractCBS Man page
sampleName.AbstractCBS Man page
sampleName<-,AbstractCBS-method Man page
sampleName,AbstractCBS-method Man page
save.AbstractCBS Man page
save,AbstractCBS-method Man page
segmentByCBS Man page
segmentByCBS.CBS Man page
segmentByCBS.CNA Man page
segmentByCBS.data.frame Man page
segmentByCBS.default Man page
segmentByNonPairedPSCBS Man page
segmentByNonPairedPSCBS.data.frame Man page
segmentByNonPairedPSCBS.default Man page
segmentByNonPairedPSCBS.PairedPSCBS Man page
segmentByPairedPSCBS Man page
segmentByPairedPSCBS.data.frame Man page
segmentByPairedPSCBS.default Man page
segmentByPairedPSCBS.PairedPSCBS Man page
seqOfSegmentsByDP Man page
seqOfSegmentsByDP.AbstractCBS Man page
seqOfSegmentsByDP.CBS Man page
seqOfSegmentsByDP.matrix Man page
seqOfSegmentsByDP.PairedPSCBS Man page
setLocusData Man page
setLocusData.AbstractCBS Man page
setLocusData,AbstractCBS-method Man page
setMeanEstimators Man page
setMeanEstimators.AbstractCBS Man page
setPloidy Man page
setPloidy.AbstractCBS Man page
setPloidy,AbstractCBS-method Man page
setSampleName Man page
setSampleName.AbstractCBS Man page
setSampleName,AbstractCBS-method Man page
setSegments Man page
setSegments.AbstractCBS Man page
setSegments,AbstractCBS-method Man page
shiftTCN Man page
shiftTCN.AbstractCBS Man page
shiftTCN.CBS Man page
shiftTCN.PairedPSCBS Man page
signalType Man page
signalType<- Man page
signalType<-.CBS Man page
signalType.CBS Man page
subset.CBS Man page
testROH Man page
testROH.numeric Man page
tileChromosomes Man page
tileChromosomes.AbstractCBS Man page
tileChromosomes.CBS Man page
tileChromosomes.PairedPSCBS Man page
unTumorBoost Man page
unTumorBoost.PairedPSCBS Man page
updateBoundaries Man page
updateBoundaries.CBS Man page
updateMeans Man page
updateMeans.AbstractCBS Man page
updateMeans,AbstractCBS-method Man page
updateMeansC1C2 Man page
updateMeansC1C2.PairedPSCBS Man page
updateMeans.CBS Man page
updateMeans.NonPairedPSCBS Man page
updateMeans.PairedPSCBS Man page
updateMeansTogether Man page
updateMeansTogether.AbstractCBS Man page
updateMeansTogether,AbstractCBS-method Man page
updateMeansTogether.CBS Man page
updateMeansTogether.PairedPSCBS Man page
weightedQuantile Man page
weightedQuantile.default Man page
writeLocusData Man page
writeLocusData.CBS Man page
writeSegments Man page
writeSegments.CBS Man page
writeSegments,CBS-method Man page
writeSegments.DNAcopy Man page
writeSegments.PSCBS Man page
writeSegments,PSCBS-method Man page
writeWIG Man page
writeWIG.AbstractCBS Man page

Files

inst
inst/CITATION
inst/misc
inst/misc/_Rcache
inst/misc/_Rcache/PSCBS
inst/misc/_Rcache/PSCBS/segmentByCBS
inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry
inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/0109d43cd74c8e7e46db1abde235c808.Rcache
inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/2aba5b85ae757609b8b4c9fc60be1156.Rcache
inst/templates
inst/templates/rsp
inst/templates/rsp/includes
inst/templates/rsp/includes/pscnSegmentationTracks.tex.rsp
inst/templates/rsp/includes/signalDensities.tex.rsp
inst/templates/rsp/includes/levelDensities.tex.rsp
inst/templates/rsp/includes/reportSetupMacros.tex.rsp
inst/templates/rsp/includes/references.tex.rsp
inst/templates/rsp/includes/summaryOfAnnotationAndGenotypeCalls.tex.rsp
inst/templates/rsp/includes/reportHeader.tex.rsp
inst/templates/rsp/includes/reportSetupGraphics.tex.rsp
inst/templates/rsp/includes/pscnSegmentationTransitions.tex.rsp
inst/templates/rsp/includes/sessionInfo.tex.rsp
inst/templates/rsp/CBS,report.tex.rsp
inst/templates/rsp/NonPairedPSCBS,report.tex.rsp
inst/templates/rsp/natbib.bst
inst/templates/rsp/PairedPSCBS,report.tex.rsp
inst/templates/rsp/bioinformatics-journals-abbr.bib
inst/templates/rsp/PSCBS.bib
inst/doc
inst/doc/CBS.R inst/doc/PairedPSCBS.R
inst/doc/CBS.pdf
inst/doc/CBS.tex.rsp
inst/doc/PairedPSCBS.tex.rsp
inst/doc/PairedPSCBS.pdf
inst/data-ex
inst/data-ex/PairedPSCBS,exData,chr01.Rbin
tests
tests/segmentByPairedPSCBS,report.R tests/segmentByCBS,shiftTCN.R tests/segmentByPairedPSCBS,noNormalBAFs.R tests/PairedPSCBS,boot.R tests/segmentByCBS,report.R tests/randomSeed.R tests/segmentByCBS.R tests/segmentByCBS,median.R tests/segmentByPairedPSCBS,DH.R tests/findLargeGaps.R tests/segmentByCBS,prune.R tests/segmentByCBS,calls.R tests/segmentByPairedPSCBS.R tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R tests/segmentByNonPairedPSCBS,medianDH.R tests/segmentByCBS,futures.R tests/segmentByPairedPSCBS,calls.R tests/segmentByPairedPSCBS,futures.R tests/segmentByCBS,weights.R
NAMESPACE
NEWS
R
R/CBS.PRUNE.R R/CBS.R R/CBS.updateMeansTogether.R R/000.R R/PairedPSCBS.PRUNE.R R/NonPairedPSCBS.R R/PairedPSCBS.applyByRegion.R R/AbstractCBS.clearCalls.R R/findNeutralCopyNumberState.R R/PairedPSCBS.callROH.R R/PairedPSCBS.estimateDeltaLOH.R R/AbstractCBS.R R/PairedPSCBS.R R/PairedPSCBS.callAB.R R/PairedPSCBS.callGNL.R R/PairedPSCBS.estimateDeltaAB.R R/PairedPSCBS.BOOT.sets.R R/999.DEPRECATED.R R/PairedPSCBS.callCopyNeutral.R R/PairedPSCBS.BOOT.R R/PairedPSCBS.unTumorBoost.R R/AbstractCBS.PLOT.R R/DNAcopy.EXTS.R R/randomSeed.R R/CBS.SMOOTH.R R/exampleData.R R/prememoize.R R/segmentByCBS.R R/CBS.joinSegments.R R/PairedPSCBS.PLOT,many.R R/installDNAcopy.R R/PSCBS.IO.R R/writeWIG.R R/segmentByNonPairedPSCBS.R R/PairedPSCBS.callLOH.R R/CBS.IO.R R/findLargeGaps.R R/weightedQuantile.R R/PairedPSCBS.updateMeansTogether.R R/PairedPSCBS.estimateKappa.R R/segmentByPairedPSCBS.R R/PairedPSCBS.EXTS.R R/AbstractCBS.RESTRUCT.R R/PairedPSCBS.CALL.R R/PSCBS.RESTRUCT.R R/PairedPSCBS.RESTRUCT.R R/006.fixVarArgs.R R/PairedPSCBS.EXTS3.R R/callSegmentationOutliers.R R/CBS.PLOT.R R/PairedPSCBS.extractSegmentDataByLocus.R R/PairedPSCBS.updateMeans.R R/AbstractCBS.REPORT.R R/CNA.EXTS.R R/PSCBS.R R/AbstractCBS.PRUNE.R R/CBS.CALL.R R/CBS.EXTS.R R/testROH.R R/PairedPSCBS.PLOT.R R/gapsToSegments.R R/drawLevels.DNAcopy.R R/AbstractCBS.HCLUST.R R/999.NonDocumentedObjects.R R/999.package.R R/CBS.PLOT,many.R R/PairedPSCBS.PLOT2.R R/zzz.R R/CBS.RESTRUCT.R
vignettes
vignettes/natbib.bst
vignettes/PSCBS.bib
vignettes/CBS.tex.rsp
vignettes/PairedPSCBS.tex.rsp
MD5
build
build/vignette.rds
DESCRIPTION
man
man/dropChangePoints.AbstractCBS.Rd man/getSmoothLocusData.CBS.Rd man/joinSegments.CBS.Rd man/as.data.frame.AbstractCBS.Rd man/randomSeed.Rd man/callAmplifications.CBS.Rd man/estimateDeltaAB.PairedPSCBS.Rd man/getFractionOfGenomeLost.CBS.Rd man/callOutliers.CBS.Rd man/exampleData.Rd man/extractMinorMajorCNs.PairedPSCBS.Rd man/gapsToSegments.data.frame.Rd man/append.PSCBS.Rd man/report.AbstractCBS.Rd man/CBS.Rd man/getSegments.PSCBS.Rd man/estimateKappa.PairedPSCBS.Rd man/ploidy.AbstractCBS.Rd man/setSampleName.AbstractCBS.Rd man/installDNAcopy.Rd man/estimateStandardDeviation.CBS.Rd man/estimateDeltaLOH.PairedPSCBS.Rd man/callGainsAndLosses.CBS.Rd man/getSegments.AbstractCBS.Rd man/mergeNonCalledSegments.CBS.Rd man/writeSegments.PSCBS.Rd man/Restructuring_AbstractCBS_objects.Rd man/callCopyNeutral.PairedPSCBS.Rd man/estimateKappaByC1Density.PairedPSCBS.Rd man/bootstrapTCNandDHByRegion.PairedPSCBS.Rd man/mergeTwoSegments.PairedPSCBS.Rd man/getBootstrapLocusSets.PairedPSCBS.Rd man/dropRegions.AbstractCBS.Rd man/load.AbstractCBS.Rd man/plotTracks.PairedPSCBS.Rd man/PSCBS-package.Rd man/callLOH.PairedPSCBS.Rd man/as.data.frame.CBS.Rd man/nbrOfSegments.AbstractCBS.Rd man/normalizeTotalCNs.AbstractCBS.Rd man/extractTCNAndDHs.PairedPSCBS.Rd man/estimateDeltaCN.PairedPSCBS.Rd man/getSampleName.AbstractCBS.Rd man/plotTracks.AbstractCBS.Rd man/estimateDeltaABBySmallDH.PairedPSCBS.Rd man/as.DNAcopy.CBS.Rd man/callAB.PairedPSCBS.Rd man/nbrOfLoci.AbstractCBS.Rd man/mergeThreeSegments.AbstractCBS.Rd man/as.CBS.DNAcopy.Rd man/updateMeansTogether.AbstractCBS.Rd man/nbrOfChromosomes.AbstractCBS.Rd man/callAllelicBalanceByDH.PairedPSCBS.Rd man/extractSegmentMeansByLocus.CBS.Rd man/mergeTwoSegments.AbstractCBS.Rd man/updateMeans.AbstractCBS.Rd man/getLocusData.AbstractCBS.Rd man/findLargeGaps.Rd man/segmentByCBS.Rd man/PairedPSCBS.Rd man/plotTracks.CBS.Rd man/pruneByDP.AbstractCBS.Rd man/estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS.Rd man/nbrOfChangePoints.AbstractCBS.Rd man/append.AbstractCBS.Rd man/segmentByNonPairedPSCBS.Rd man/callROH.PairedPSCBS.Rd man/testROH.numeric.Rd man/append.CBS.Rd man/pruneBySdUndo.CBS.Rd man/AbstractCBS.Rd man/save.AbstractCBS.Rd man/weightedQuantile.Rd man/writeSegments.CBS.Rd man/PSCBS.Rd man/getChromosomes.AbstractCBS.Rd man/callSegmentationOutliers.Rd man/getCallStatistics.CBS.Rd man/hclustCNs.AbstractCBS.Rd man/segmentByPairedPSCBS.Rd man/resetSegments.AbstractCBS.Rd man/NonPairedPSCBS.Rd man/callGNL.PairedPSCBS.Rd man/callCopyNeutralByTCNofAB.PairedPSCBS.Rd man/findNeutralCopyNumberState.Rd man/pruneByHClust.AbstractCBS.Rd man/Non-documented_objects.Rd

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