AbstractCBS: The AbstractCBS class

Description Usage Arguments Fields and Methods Author(s)

Description

Package: PSCBS
Class AbstractCBS

list
~~|
~~+--AbstractCBS

Directly known subclasses:
CBS, NonPairedPSCBS, PSCBS, PairedPSCBS

public abstract static class AbstractCBS
extends list

All CBS-style segmentation results extend this class, e.g. CBS and PairedPSCBS.

Usage

1

Arguments

fit

A list structure containing the segmentation results.

sampleName

A character string.

...

Not used.

Fields and Methods

Methods:

adjustPloidyScale -
append Appends one segmentation result to another.
extractCNs -
getChangePoints -
getChromosomes Gets the set of chromosomes.
getLocusData Gets the locus-level data.
getSegmentSizes -
getSegments Gets the segments.
load Loads an AbstractCBS object from file.
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 -
save Saves an AbstractCBS object to file.
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, wrap

Author(s)

Henrik Bengtsson


PSCBS documentation built on May 6, 2019, 1:05 a.m.