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

AbstractCBS

R Documentation

The AbstractCBS class

Description

Package: PSCBS
Class AbstractCBS

list
~~|
~~+--AbstractCBS

Directly known subclasses:
CBS, NonPairedPSCBS, PSCBS, PairedPSCBS

public abstract class AbstractCBS
extends list

All CBS-style segmentation results extend this class, e.g. CBS and PairedPSCBS.

Usage

AbstractCBS(fit=list(), sampleName=fit$sampleName, ...)

Arguments

`fit`	A `list` structure containing the segmentation results.
`sampleName`	A `character` string.
`...`	Not used.

Fields and Methods

Methods:

	`adjustPloidyScale`	-
	`extractCNs`	-
	`getChangePoints`	-
	`getChromosomes`	Gets the set of chromosomes.
	`getLocusData`	Gets the locus-level data.
	`getSegmentSizes`	-
	`getSegments`	Gets the segments.
	`mergeThreeSegments`	Merge a segment and its two flanking segments.
	`nbrOfChangePoints`	Gets the number of change points.
	`nbrOfChromosomes`	Gets the number of chromosomes.
	`nbrOfLoci`	Gets the number of loci.
	`nbrOfSegments`	Gets the number of segments.
	`normalizeTotalCNs`	Normalizes copy numbers such that the whole-genome average total copy number is two.
	`ploidy`	Gets and sets ploidy.
	`ploidy<-`	-
	`plotTracks`	Plots the segmentation result along the genome.
	`sampleCNs`	-
	`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