PairedPSCBS: The PairedPSCBS class
Description
Package: PSCBS
Class PairedPSCBS
list
~~|
~~+--AbstractCBS
~~~~~~~|
~~~~~~~+--PSCBS
~~~~~~~~~~~~|
~~~~~~~~~~~~+--PairedPSCBS
Directly known subclasses:
public abstract static class PairedPSCBS
extends PSCBS
A PairedPSCBS is an object containing the results from the
Paired PSCBS method.Usage
PairedPSCBS(fit=list(), ...)
Arguments
fit
A list structure containing the Paired PSCBS results. Fields and Methods
Methods:
rll{
callAB Calls segments that are in allelic balance.
callCN Calls segments that are copy neutral.
callCopyNeutral -
callGainNeutralLoss -
callGNL Calls segments that are gained, copy neutral, or lost.
callLOH Calls segments that are in LOH.
callROH Calls segments that are in ROH.
estimateDeltaAB Estimate a threshold for calling allelic balance from DH.
estimateDeltaLOH Estimate a threshold for calling LOH from DH.
estimateKappa Estimate global background in segmented copy numbers.
extractCNs -
getSegmentSizes -
plotTracks Plots parental specific copy numbers along the genome.
segmentByPairedPSCBS -
}
Methods inherited from PSCBS:
append, as.data.frame, drawChangePoints, extractChromosomes, getLocusData, isSegmentSplitter, writeSegments
Methods inherited from AbstractCBS:
all.equal, append, as.data.frame, drawChangePoints, dropChangePoint, dropChangePoints, dropRegion, dropRegions, extractChromosome, extractChromosomes, extractCNs, extractRegions, extractSegments, getChromosomes, getLocusData, getSampleName, getSegments, getSegmentSizes, load, mergeThreeSegments, mergeTwoSegments, nbrOfChangePoints, nbrOfChromosomes, nbrOfLoci, nbrOfSegments, plotTracks, print, pruneByHClust, renameChromosomes, resegment, sampleCNs, sampleName, sampleName<-, save, setLocusData, setSampleName, setSegments, tileChromosomes, updateMeans
Methods inherited from list:
all.equal, as.data.frame, attachLocally, callHooks, relist, within