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aroma.core (version 3.0.0)

NonPairedPSCNData: The NonPairedPSCNData class

Description

Package: aroma.core Class NonPairedPSCNData

data.frame ~~| ~~+--RichDataFrame ~~~~~~~| ~~~~~~~+--RawGenomicSignals ~~~~~~~~~~~~| ~~~~~~~~~~~~+--AbstractCNData ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--AbstractPSCNData ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--NonPairedPSCNData

Directly known subclasses:

public class NonPairedPSCNData extends AbstractPSCNData

A NonPairedPSCNData object holds parent-specific copy number data. Two NonPairedPSCNData objects for a matched tumor-normal pair can be combined into a PairedPSCNData object.

Usage

NonPairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, C=NULL, beta=NULL, ...)

Arguments

C
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.
beta
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.
mu
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.
x
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.NonPairedPSCNData -
as.PairedPSCNData
-
callNaiveGenotypes -
callSegmentationOutliers
-
dropSegmentationOutliers -
getSignalColumnNames
-
segmentByCBS -
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