PairedPSCBS: The PairedPSCBS class

PairedPSCBSR Documentation

The PairedPSCBS class

Description

Package: PSCBS
Class PairedPSCBS

list
~~|
~~+--AbstractCBS
~~~~~~~|
~~~~~~~+--PSCBS
~~~~~~~~~~~~|
~~~~~~~~~~~~+--PairedPSCBS

Directly known subclasses:

public abstract 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:
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, callHooks, coerce,ANY,list-method, relist, type.convert, within

Author(s)

Henrik Bengtsson

See Also

The segmentByPairedPSCBS() method returns an object of this class.


PSCBS documentation built on May 29, 2024, 5:59 a.m.