PairedPSCBS: The PairedPSCBS class
In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Description Usage Arguments Fields and Methods Author(s) See Also

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.

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

`fit`	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`	Plots parental specific copy numbers along the genome.
	`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, 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:
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, coerce,Matrix,vector-method, coerce,abIndex,vector-method, coerce,dgCMatrix,vector-method, coerce,dsCMatrix,vector-method, coerce,list,indMatrix-method, coerce,sparseVector,vector-method, contents, ggplot_add, latex, normalizeAverage, normalizeDifferencesToAverage, normalizeQuantileRank, normalizeQuantileSpline, plotDensity, relist, scale_type, type.convert, within

Henrik Bengtsson

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

PSCBS documentation built on Oct. 23, 2021, 9:09 a.m.