NonPairedPSCNData {aroma.core}R Documentation

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:
$<-,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, 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

Author(s)

Henrik Bengtsson


[Package aroma.core version 3.2.2 Index]