PSCBS (version 0.38.4)

CBS: 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 static class CBS extends AbstractCBS

Usage

CBS(...)

Arguments

...

Arguments passed to the constructor of AbstractCBS.

Fields and Methods

Methods: rll{ append Appends one segmentation result to another. as - 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, drawChangePoints, drawKnownSegments, dropChangePoint, dropChangePoints, dropRegion, dropRegions, extractCNs, extractChromosome, extractChromosomes, extractRegions, extractSegments, getChromosomeOffsets, getChromosomeRanges, getChromosomes, getLocusData, getLocusSignalNames, getMeanEstimators, getSampleName, getSegmentSizes, getSegmentTrackPrefixes, getSegments, load, mergeThreeSegments, mergeTwoSegments, nbrOfChangePoints, nbrOfChromosomes, nbrOfLoci, nbrOfSegments, ploidy, ploidy<-, plotTracks, print, pruneByDP, pruneByHClust, renameChromosomes, report, resegment, resetSegments, sampleCNs, sampleName, sampleName<-, save, seqOfSegmentsByDP, setLocusData, setMeanEstimators, setPloidy, setSampleName, setSegments, shiftTCN, tileChromosomes, updateMeans

Methods inherited from list: all.equal, as.data.frame, attachLocally, callHooks, relist, 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.