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

CBS	R Documentation

The CBS class

Description

A CBS object holds results from the Circular Binary Segmentation (CBS) method for one sample for one or more chromosomes.

Package: PSCBS
Class CBS

list
~~|
~~+--AbstractCBS
~~~~~~~|
~~~~~~~+--CBS

Directly known subclasses:

public abstract class CBS
extends AbstractCBS

Usage

CBS(...)

Arguments

...

Arguments passed to the constructor of AbstractCBS.

Fields and Methods

Methods:

	`as`	-
	`c`	-
	`estimateStandardDeviation`	-
	`plotTracks`	-
	`pruneBySdUndo`	-
	`segmentByCBS`	-
	`seqOfSegmentsByDP`	-
	`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

Difference to DNAcopy object

A CBS object is similar to DNAcopy objects with the major difference that a CBS object holds only one sample, whereas a DNAcopy object can hold more than one sample.