NonPairedPSCBS: The NonPairedPSCBS class

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Description

Package: PSCBS
Class NonPairedPSCBS

list
~~|
~~+--AbstractCBS
~~~~~~~|
~~~~~~~+--PSCBS
~~~~~~~~~~~~|
~~~~~~~~~~~~+--NonPairedPSCBS

Directly known subclasses:

public abstract static class NonPairedPSCBS
extends PSCBS

A NonPairedPSCBS is an object containing the results from the Non-paired PSCBS method.

Usage

NonPairedPSCBS(fit=list(), ...)

Arguments

fit	A list structure containing the Non-paired PSCBS results.
...	Not used.

Fields and Methods

Methods:
No methods defined.

Methods inherited from PSCBS:
as.data.frame, c, drawChangePoints, extractChromosomes, extractWIG, getLocusData, getLocusSignalNames, getSegmentTrackPrefixes, isLocallyPhased, isSegmentSplitter, normalizeTotalCNs, writeSegments

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

Author(s)

Henrik Bengtsson

See Also

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

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