PairedPSCBS: The PairedPSCBS class

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

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.

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.