Files in PSCBS

Analysis of Parent-Specific DNA Copy Numbers

NEWS.md README.md R/segmentByNonPairedPSCBS.R R/segmentByPairedPSCBS.R R/PSCBS.R R/weightedQuantile.R R/PairedPSCBS.callCopyNeutral.R R/PairedPSCBS.updateMeans.R R/AbstractCBS.PRUNE.R R/segmentByCBS.R R/AbstractCBS.R R/PairedPSCBS.extractSegmentDataByLocus.R R/PairedPSCBS.BOOT.sets.R R/NonPairedPSCBS.R R/CBS.PLOT.R R/PairedPSCBS.estimateDeltaAB.R R/PSCBS.isLocallyPhased.R R/gapsToSegments.R R/CBS.PLOT,many.R R/PairedPSCBS.callLOH.R R/CBS.EXTS.R R/PairedPSCBS.estimateKappa.R R/PairedPSCBS.callROH.R R/PairedPSCBS.applyByRegion.R R/PairedPSCBS.R R/PairedPSCBS.callGNL.R R/installDNAcopy.R R/PSCBS.IO.R R/prememoize.R R/PairedPSCBS.callAB.R R/CBS.RESTRUCT.R R/CBS.IO.R R/exampleData.R R/PairedPSCBS.PLOT.R R/drawLevels.DNAcopy.R R/CBS.joinSegments.R R/999.package.R R/AbstractCBS.REPORT.R R/PSCBS.RESTRUCT.R R/PairedPSCBS.updateMeansTogether.R R/000.R R/CBS.SMOOTH.R R/PairedPSCBS.BOOT.R R/PairedPSCBS.estimateDeltaLOH.R R/PairedPSCBS.PLOT2.R R/findLargeGaps.R R/PairedPSCBS.unTumorBoost.R R/PairedPSCBS.RESTRUCT.R R/CNA.EXTS.R R/PairedPSCBS.EXTS.R R/AbstractCBS.RESTRUCT.R R/AbstractCBS.HCLUST.R R/AbstractCBS.clearCalls.R R/CBS.updateMeansTogether.R R/testROH.R R/999.NonDocumentedObjects.R R/DNAcopy.EXTS.R R/zzz.R R/callSegmentationOutliers.R R/CBS.R R/randomSeed.R R/writeWIG.R R/CBS.PRUNE.R R/findNeutralCopyNumberState.R R/999.DEPRECATED.R R/PairedPSCBS.CALL.R R/PairedPSCBS.PRUNE.R R/PairedPSCBS.PLOT,many.R R/utils.R R/CBS.CALL.R R/PairedPSCBS.EXTS3.R R/AbstractCBS.PLOT.R inst/doc/CBS.pdf inst/doc/PairedPSCBS.R inst/doc/CBS.R inst/doc/PairedPSCBS.pdf tests/segmentByPairedPSCBS.R tests/segmentByPairedPSCBS,futures.R tests/segmentByPairedPSCBS,noNormalBAFs.R tests/segmentByCBS,shiftTCN.R tests/segmentByCBS.R tests/segmentByPairedPSCBS,calls.R tests/segmentByCBS,prune.R tests/segmentByPairedPSCBS,report.R tests/PairedPSCBS,boot.R tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R tests/segmentByCBS,report.R tests/findLargeGaps.R tests/segmentByCBS,weights.R tests/segmentByCBS,median.R tests/segmentByPairedPSCBS,DH.R tests/segmentByNonPairedPSCBS,medianDH.R tests/randomSeed.R tests/segmentByCBS,calls.R tests/segmentByCBS,futures.R man/gapsToSegments.data.frame.Rd man/joinSegments.CBS.Rd man/segmentByCBS.Rd man/extractSegmentMeansByLocus.CBS.Rd man/extractTCNAndDHs.PairedPSCBS.Rd man/callGainsAndLosses.CBS.Rd man/callROH.PairedPSCBS.Rd man/plotTracks.CBS.Rd man/getBootstrapLocusSets.PairedPSCBS.Rd man/Non-documented_objects.Rd man/estimateDeltaABBySmallDH.PairedPSCBS.Rd man/callCopyNeutralByTCNofAB.PairedPSCBS.Rd man/callAmplifications.CBS.Rd man/c.CBS.Rd man/resetSegments.AbstractCBS.Rd man/as.data.frame.AbstractCBS.Rd man/getCallStatistics.CBS.Rd man/writeSegments.PSCBS.Rd man/dropRegions.AbstractCBS.Rd man/normalizeTotalCNs.AbstractCBS.Rd man/plotTracks.AbstractCBS.Rd man/report.AbstractCBS.Rd man/getChromosomes.AbstractCBS.Rd man/testROH.numeric.Rd man/updateMeans.AbstractCBS.Rd man/ploidy.AbstractCBS.Rd man/PSCBS.Rd man/nbrOfLoci.AbstractCBS.Rd man/callSegmentationOutliers.Rd man/nbrOfChangePoints.AbstractCBS.Rd man/callGNL.PairedPSCBS.Rd man/getFractionOfGenomeLost.CBS.Rd man/findNeutralCopyNumberState.Rd man/getSegments.PSCBS.Rd man/mergeTwoSegments.PairedPSCBS.Rd man/updateMeansTogether.AbstractCBS.Rd man/getLocusData.AbstractCBS.Rd man/nbrOfSegments.AbstractCBS.Rd man/estimateDeltaCN.PairedPSCBS.Rd man/estimateKappa.PairedPSCBS.Rd man/as.CBS.DNAcopy.Rd man/estimateDeltaLOH.PairedPSCBS.Rd man/mergeThreeSegments.AbstractCBS.Rd man/estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS.Rd man/bootstrapTCNandDHByRegion.PairedPSCBS.Rd man/installDNAcopy.Rd man/estimateKappaByC1Density.PairedPSCBS.Rd man/hclustCNs.AbstractCBS.Rd man/getSegments.AbstractCBS.Rd man/pruneBySdUndo.CBS.Rd man/getSmoothLocusData.CBS.Rd man/weightedQuantile.Rd man/getSampleName.AbstractCBS.Rd man/callAllelicBalanceByDH.PairedPSCBS.Rd man/plotTracks1.PairedPSCBS.Rd man/callOutliers.CBS.Rd man/pruneByDP.AbstractCBS.Rd man/dropChangePoints.AbstractCBS.Rd man/segmentByPairedPSCBS.Rd man/NonPairedPSCBS.Rd man/PSCBS-package.Rd man/estimateDeltaAB.PairedPSCBS.Rd man/nbrOfChromosomes.AbstractCBS.Rd man/CBS.Rd man/setSampleName.AbstractCBS.Rd man/exampleData.Rd man/writeSegments.CBS.Rd man/callLOH.PairedPSCBS.Rd man/AbstractCBS.Rd man/pruneByHClust.AbstractCBS.Rd man/estimateStandardDeviation.CBS.Rd man/Restructuring_AbstractCBS_objects.Rd man/callAB.PairedPSCBS.Rd man/callCopyNeutral.PairedPSCBS.Rd man/randomSeed.Rd man/mergeTwoSegments.AbstractCBS.Rd man/mergeNonCalledSegments.CBS.Rd man/findLargeGaps.Rd man/segmentByNonPairedPSCBS.Rd man/as.data.frame.CBS.Rd man/PairedPSCBS.Rd man/extractMinorMajorCNs.PairedPSCBS.Rd man/as.DNAcopy.CBS.Rd