PairedPSCNData: 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

A numeric vector of J tumor total copy number (TCN) ratios in [0,+Inf) (due to noise, small negative values are also allowed). The TCN ratios are typically scaled such that copy-neutral diploid loci have a mean of two.

An optional numeric vector of J normal TCN ratios.

betaT

A numeric vector of J tumor allele B fractions (BAFs) in [0,1] (due to noise, values may be slightly outside as well) or NA for non-polymorphic loci.

betaN

A numeric vector of J matched normal BAFs in [0,1] (due to noise, values may be slightly outside as well) or NA for non-polymorphic loci.

muN

An optional numeric vector of J genotype calls in {0,1/2,1} for AA, AB, and BB, respectively, and NA for non-polymorphic loci. If not given, they are estimated from the normal BAFs using callNaiveGenotypes as described in [2].

isSNP

An optional logical vector of length J specifying whether each locus is a SNP or not (non-polymorphic loci).

chromosome

(Optional) An integer scalar (or a vector of length J), which can be used to specify which chromosome each locus belongs to in case multiple chromosomes are segments. This argument is also used for annotation purposes.

Optional numeric vector of J genomic locations. If NULL, index locations 1:J are used.

...

Optional named locus-specific signal vectors of length J.

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: $, $<-, Math, Ops, Summary, [, [<-, [[, [[<-, aggregate, anyDuplicated, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, attachLocally, by, callSegmentationOutliers, cbind, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, split, split<-, stack, str, subset, summary, t, tail, transform, unique, unstack, unwrap, within, wrap, writeDataFrame