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 noi

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

betaN

A numeric vector of J matched normal BAFs in [0,1] (due to noise, values may be slightly outside as well) or

muN

An optional numeric vector of J genotype calls in {0,1/2,1} for AA, AB, and BB, respectively, and

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

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

...

Optional named locus-specific signal vectors of length J.

Fields and Methods

Methods: rll{ as - as.PairedPSCNData - callNaiveGenotypes - callSegmentationOutliers - dropSegmentationOutliers - getSignalColumnNames - getTCNs - getTotalCopyNumbers - normalizeTumorBoost - plotTracks Plots parental specific copy numbers along the genome. 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.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getChromosome, getChromosomes, getCXY, 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: $<-, [, [[, [[<-, [<-, aggregate, anyDuplicated, as.data.frame, as.list, as.matrix, as.NonPairedPSCNData, as.PairedPSCNData, attachLocally, by, cbind, dim, dimnames, dimnames<-, droplevels, duplicated, edit, format, formula, head, is.na, Math, mean, merge, na.exclude, na.omit, Ops, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, split, split<-, stack, str, subset, summary, Summary, t, tail, transform, unique, unstack, unwrap, within, wrap, writeDataFrame