CBS: The CBS class

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

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 static class CBS
extends AbstractCBS

Usage

CBS(...)

Arguments

...	Arguments passed to the constructor of AbstractCBS.

Fields and Methods

Methods:

	as	-
	c	Concatenates segmentation results.
	estimateStandardDeviation	Estimates the whole-genome standard deviation of the signals.
	plotTracks	Plots copy numbers along the genome.
	pruneBySdUndo	Prune the CBS profile by dropping change points that are too small.
	segmentByCBS	-
	seqOfSegmentsByDP	-
	writeSegments	Writes the table of segments to file.

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

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.

See also

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

Author(s)

Henrik Bengtsson

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