PairedPSCBS: The PairedPSCBS class

Description

Package: PSCBS Class PairedPSCBS

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.

Usage

PairedPSCBS(fit=list(), ...)

Arguments

fit

A list structure containing the Paired PSCBS results.

...

Not used.

Fields and Methods

Methods:

	`callAB`	-
	`callCopyNeutral`	-
	`callGNL`	-
	`callGNLByTCNofAB`	-
	`callGainNeutralLoss`	-
	`callLOH`	-
	`callNTCN`	-
	`callROH`	-
	`estimateDeltaAB`	-
	`estimateDeltaLOH`	-
	`estimateKappa`	-
	`extractCNs`	-
	`hasBootstrapSummaries`	-
	`plotTracks`	-
	`segmentByNonPairedPSCBS`	-
	`segmentByPairedPSCBS`	-
	`seqOfSegmentsByDP`	-

Methods inherited from PSCBS: append, as.data.frame, drawChangePoints, extractChromosomes, extractWIG, getLocusData, getLocusSignalNames, getSegmentTrackPrefixes, isLocallyPhased, isSegmentSplitter, normalizeTotalCNs, writeSegments

Methods inherited from AbstractCBS: adjustPloidyScale, all.equal, append, 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, load, mergeThreeSegments, mergeTwoSegments, nbrOfChangePoints, nbrOfChromosomes, nbrOfLoci, nbrOfSegments, normalizeTotalCNs, ploidy, ploidy<-, plotTracks, print, pruneByDP, pruneByHClust, renameChromosomes, report, resegment, resetSegments, sampleCNs, sampleName, sampleName<-, save, seqOfSegmentsByDP, setLocusData, setMeanEstimators, setPloidy, setSampleName, setSegments, shiftTCN, tileChromosomes, updateMeans, writeWIG

Methods inherited from list: all.equal, as.data.frame, attachLocally, callHooks, relist, within

Description

Usage

Arguments

Fields and Methods

See Also