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 |
sampleName |
A |
... |
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
Henrik Bengtsson
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