PairedPSCNData {aroma.core} | R Documentation |
The PairedPSCNData class
Description
Package: aroma.core
Class PairedPSCNData
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AbstractPSCNData
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
PairedPSCNData
Directly known subclasses:
public class PairedPSCNData
extends AbstractPSCNData
A PairedPSCNData object holds paired tumor-normal parent-specific copy number data.
Usage
PairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, muN=NULL, CT=NULL, betaT=NULL,
CN=NULL, betaN=NULL, ...)
Arguments
CT |
A |
CN |
|
betaT |
A |
betaN |
A |
muN |
An optional |
isSNP |
An optional |
chromosome |
(Optional) An |
x |
Optional |
... |
Optional named locus-specific signal |
Fields and Methods
Methods:
as | - | |
as.PairedPSCNData | - | |
callNaiveGenotypes | - | |
callSegmentationOutliers | - | |
dropSegmentationOutliers | - | |
getSignalColumnNames | - | |
getTCNs | - | |
getTotalCopyNumbers | - | |
normalizeTumorBoost | - | |
plotTracks | - | |
segmentByCBS | - | |
segmentByPairedPSCBS | - | |
Methods inherited from AbstractPSCNData:
callSNPs, getSNPFields
Methods inherited from AbstractCNData:
findLargeGaps, getChipType, getLocusData, getPlatform, hasKnownPositions, orderAlongGenome, setChipType, setPlatform
Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange
Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames
Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Author(s)
Henrik Bengtsson