AbstractCBS: The AbstractCBS class
In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Description Usage Arguments Fields and Methods Author(s)

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.

1	AbstractCBS(fit=list(), sampleName=fit$sampleName, ...)

`fit`	A `list` structure containing the segmentation results.
`sampleName`	A `character` string.
`...`	Not used.

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

Henrik Bengtsson

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