PSCBS: Analysis of Parent-Specific DNA Copy Numbers

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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.

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]
Date of publication
2016-11-11 00:23:02
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
GPL (>= 2)
Version
0.62.0
URLs

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

Files in this package

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