PSCBS: The PSCBS class

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

The PSCBS class

Description

Package: PSCBS
Class PSCBS

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

Directly known subclasses:
NonPairedPSCBS, PairedPSCBS

public abstract class PSCBS
extends AbstractCBS

A PSCBS is an object containing results from parent-specific copy-number (PSCN) segmentation.

Usage

PSCBS(fit=list(), ...)

Arguments

fit	A list structure containing the PSCN segmentation results.
...	Not used.

Fields and Methods

Methods:

	c	-
	isLocallyPhased	-
	normalizeTotalCNs	-
	writeSegments	Writes the table of segments to file.

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, averageQuantile, callHooks, coerce,ANY,list-method, normalizeAverage, normalizeDifferencesToAverage, normalizeQuantileRank, normalizeQuantileSpline, plotDensity, relist, reset, type.convert, within

Author(s)

Henrik Bengtsson

See Also

PairedPSCBS.

PSCBS documentation built on June 8, 2025, 11:44 a.m.