AbstractCBS: The AbstractCBS class

AbstractCBSR 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

Author(s)

Henrik Bengtsson


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