Man pages for HenrikBengtsson/PSCBS
Analysis of Parent-Specific DNA Copy Numbers

AbstractCBSThe AbstractCBS class
append.AbstractCBSAppends one segmentation result to another
append.CBSAppends one segmentation result to another
append.PSCBSAppends one segmentation result to another
as.CBS.DNAcopyCoerces a DNAcopy object to a CBS object the table of segments the table of segments
as.DNAcopy.CBSCoerces a CBS object to a DNAcopy object
bootstrapTCNandDHByRegion.PairedPSCBSEstimate confidence intervals of TCN and DH segment levels
callAB.PairedPSCBSCalls segments that are in allelic balance
callAllelicBalanceByDH.PairedPSCBSCalls segments that are in allelic balance
callAmplifications.CBSCalls (focal) amplifications
callCopyNeutralByTCNofAB.PairedPSCBSCalls regions that are copy neutral
callCopyNeutral.PairedPSCBSCalls segments that have a neutral total copy number
callGainsAndLosses.CBSCalls gains and losses
callGNL.PairedPSCBSCalls segments that are gained, copy neutral, or lost
callLOH.PairedPSCBSCalls segments that are in LOH
callOutliers.CBSCalls outliers
callROH.PairedPSCBSCalls segments that are in ROH
callSegmentationOutliersCalls/drops single-locus outliers along the genome
CBSThe CBS class
dropChangePoints.AbstractCBSDrops zero or more change points
dropRegions.AbstractCBSDrops chromosomal regions (a connected set of segments)
estimateDeltaABBySmallDH.PairedPSCBSEstimate a threshold for calling allelic balance from DH
estimateDeltaAB.PairedPSCBSEstimate a threshold for calling allelic balance from DH
estimateDeltaCN.PairedPSCBSEstimates the length of one total copy-number (TCN) unit
estimateDeltaLOHByMinC1ForNonAB.PairedPSCBSEstimate a threshold for calling LOH from DH
estimateDeltaLOH.PairedPSCBSEstimate a threshold for calling LOH from DH
estimateKappaByC1Density.PairedPSCBSEstimate global background in segmented copy numbers
estimateKappa.PairedPSCBSEstimate global background in segmented copy numbers
estimateStandardDeviation.CBSEstimates the whole-genome standard deviation of the signals
exampleDataGets an example data set
extractMinorMajorCNs.PairedPSCBSExtract minor and major copy-number mean levels per segment
extractSegmentMeansByLocus.CBSExtracts segments means at each locus
extractTCNAndDHs.PairedPSCBSExtract TCN and DH mean levels per segment
findLargeGapsIdentifies gaps of a genome where there exist no observations
findNeutralCopyNumberStateCall segments to be copy neutral based on allelic imbalance... the genomic segments that are complementary to the gaps
getBootstrapLocusSets.PairedPSCBSGenerates original and bootstrapped segment-specific index...
getCallStatistics.CBSCalculates various call statistics per chromosome
getChromosomes.AbstractCBSGets the set of chromosomes
getFractionOfGenomeLost.CBSCalculates the fraction of the genome lost, gained, or...
getLocusData.AbstractCBSGets the locus-level data
getSampleName.AbstractCBSGets the name of the sample segmented
getSegments.AbstractCBSGets the segments
getSegments.PSCBSGets the segments
getSmoothLocusData.CBSGets smoothed locus-level data
hclustCNs.AbstractCBSPerforms a hierarchical clustering of the CN mean levels
installDNAcopyInstall the DNAcopy package
joinSegments.CBSJoins neighboring segments such that there is no gap in...
load.AbstractCBSLoads an AbstractCBS object from file
mergeNonCalledSegments.CBSMerge neighboring segments that are not called
mergeThreeSegments.AbstractCBSMerge a segment and its two flanking segments
mergeTwoSegments.AbstractCBSMerge two neighboring segments
mergeTwoSegments.PairedPSCBSMerge two neighboring segments
nbrOfChangePoints.AbstractCBSGets the number of change points
nbrOfChromosomes.AbstractCBSGets the number of chromosomes
nbrOfLoci.AbstractCBSGets the number of loci
nbrOfSegments.AbstractCBSGets the number of segments
Non-documented_objectsNon-documented objects
NonPairedPSCBSThe NonPairedPSCBS class
normalizeTotalCNs.AbstractCBSNormalizes copy numbers such that the whole-genome average...
PairedPSCBSThe PairedPSCBS class
ploidy.AbstractCBSGets and sets ploidy
plotTracks.AbstractCBSPlots the segmentation result along the genome
plotTracks.CBSPlots copy numbers along the genome
plotTracks.PairedPSCBSPlots parental specific copy numbers along the genome
pruneByDP.AbstractCBSPrunes the CN profile using dynamical programming
pruneByHClust.AbstractCBSPrunes the CN profile by pruning and merging through...
pruneBySdUndo.CBSPrune the CBS profile by dropping change points that are too...
PSCBS-packagePackage PSCBS
randomSeedSets and resets the .Random.seed in the global environment
report.AbstractCBSGenerates a report of the segmentation results
resetSegments.AbstractCBSReset the segments
Restructuring_AbstractCBS_objectsRestructuring AbstractCBS objects
save.AbstractCBSSaves an AbstractCBS object to file
segmentByCBSSegment genomic signals using the CBS method
segmentByNonPairedPSCBSSegment total copy numbers and allele B fractions using the...
segmentByPairedPSCBSSegment total copy numbers and allele B fractions using the...
setSampleName.AbstractCBSSets the name of the sample segmented
testROH.numericTests if a segment is in Run-of-Homozygosity (ROH)
updateMeans.AbstractCBSUpdates the CN mean levels for each segment independently
updateMeansTogether.AbstractCBSUpdates the CN mean levels jointly in sets of segments
weightedQuantileWeighted Quantile Value
writeSegments.CBSWrites the table of segments to file
writeSegments.PSCBSWrites the table of segments to file
HenrikBengtsson/PSCBS documentation built on July 1, 2017, 1:08 p.m.