list
~~|
~~+--AbstractCBS
~~~~~~~|
~~~~~~~+--PSCBS
~~~~~~~~~~~~|
~~~~~~~~~~~~+--PairedPSCBS
Directly known subclasses:
public abstract static class PairedPSCBS
extends PSCBS
A PairedPSCBS is an object containing the results from the
Paired PSCBS method.PairedPSCBS(fit=list(), ...)list structure containing the Paired PSCBS results.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 -
plotTracks Plots parental specific copy numbers along the genome.
segmentByNonPairedPSCBS -
segmentByPairedPSCBS -
seqOfSegmentsByDP -
}Methods inherited from PSCBS: append, as.data.frame, drawChangePoints, extractChromosomes, getLocusData, getLocusSignalNames, getSegmentTrackPrefixes, isSegmentSplitter, writeSegments
Methods inherited from AbstractCBS: adjustPloidyScale, all.equal, append, as.data.frame, drawChangePoints, drawKnownSegments, dropChangePoint, dropChangePoints, dropRegion, dropRegions, extractCNs, extractChromosome, extractChromosomes, extractRegions, extractSegments, getChromosomeOffsets, getChromosomeRanges, getChromosomes, getLocusData, getLocusSignalNames, getMeanEstimators, getSampleName, getSegmentSizes, getSegmentTrackPrefixes, getSegments, load, mergeThreeSegments, mergeTwoSegments, nbrOfChangePoints, nbrOfChromosomes, nbrOfLoci, nbrOfSegments, ploidy, ploidy<-, plotTracks, print, pruneByDP, pruneByHClust, renameChromosomes, report, resegment, resetSegments, sampleCNs, sampleName, sampleName<-, save, seqOfSegmentsByDP, setLocusData, setMeanEstimators, setPloidy, setSampleName, setSegments, shiftTCN, tileChromosomes, updateMeans
Methods inherited from list: all.equal, as.data.frame, attachLocally, callHooks, relist, within
segmentByPairedPSCBS() method returns an object of this class.