Package: PSCBS
Class PairedPSCBS
list
~~|
~~+--AbstractCBS
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~~~~~~~+--PSCBS
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~~~~~~~~~~~~+--PairedPSCBS
Directly known subclasses:
public abstract class PairedPSCBS
extends PSCBS
A PairedPSCBS is an object containing the results from the Paired PSCBS method.
PairedPSCBS(fit=list(), ...)
A list structure containing the Paired PSCBS results.
Not used.
Methods:
callAB | Calls segments that are in allelic balance. | |
callCopyNeutral | Calls segments that have a neutral total copy number. | |
callGNL | Calls segments that are gained, copy neutral, or lost. | |
callGNLByTCNofAB | - | |
callGainNeutralLoss | - | |
callLOH | Calls segments that are in LOH. | |
callNTCN | - | |
callROH | Calls segments that are in ROH. | |
estimateDeltaAB | Estimate a threshold for calling allelic balance from DH. | |
estimateDeltaLOH | Estimate a threshold for calling LOH from DH. | |
estimateKappa | Estimate global background in segmented copy numbers. | |
extractCNs | - | |
hasBootstrapSummaries | - | |
plotTracks | - | |
segmentByNonPairedPSCBS | - | |
segmentByPairedPSCBS | - | |
seqOfSegmentsByDP | - |
Methods inherited from PSCBS:
as.data.frame, c, drawChangePoints, extractChromosomes, extractWIG, getLocusData, getLocusSignalNames, getSegmentTrackPrefixes, isLocallyPhased, isSegmentSplitter, normalizeTotalCNs, writeSegments
Methods inherited from AbstractCBS:
adjustPloidyScale, all.equal, as.data.frame, clearCalls, drawChangePoints, drawKnownSegments, dropChangePoint, dropChangePoints, dropRegion, dropRegions, extractCNs, extractChromosome, extractChromosomes, extractRegions, extractSegments, extractWIG, getChangePoints, getChromosomeOffsets, getChromosomeRanges, getChromosomes, getLocusData, getLocusSignalNames, getMeanEstimators, getSampleName, getSegmentSizes, getSegmentTrackPrefixes, getSegments, mergeThreeSegments, mergeTwoSegments, nbrOfChangePoints, nbrOfChromosomes, nbrOfLoci, nbrOfSegments, normalizeTotalCNs, ploidy, ploidy<-, plotTracks, print, pruneByDP, pruneByHClust, renameChromosomes, report, resegment, resetSegments, sampleCNs, sampleName, sampleName<-, seqOfSegmentsByDP, setLocusData, setMeanEstimators, setPloidy, setSampleName, setSegments, shiftTCN, tileChromosomes, updateMeans, writeWIG
Methods inherited from list:
Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, all.equal, as.data.frame, attachLocally, averageQuantile, callHooks, coerce,ANY,list-method, normalizeAverage, normalizeDifferencesToAverage, normalizeQuantileRank, normalizeQuantileSpline, plotDensity, relist, reset, type.convert, within
Henrik Bengtsson
The segmentByPairedPSCBS() method returns an object of this class.