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
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~~+--AbstractCBS
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~~~~~~~+--CBS
Directly known subclasses:
public abstract static class CBS extends AbstractCBS
CBS(...)Arguments passed to the constructor of AbstractCBS.
Methods:
append |
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as |
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estimateStandardDeviation |
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plotTracks |
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pruneBySdUndo |
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segmentByCBS |
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seqOfSegmentsByDP |
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writeSegments |
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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: all.equal, as.data.frame, attachLocally, callHooks, relist, within
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.
The segmentByCBS() method returns an object of this class.