RawGenomicSignals: The RawGenomicSignals class

Description

Package: aroma.core Class RawGenomicSignals

data.frame ~~| ~~+--RichDataFrame ~~~~~~~| ~~~~~~~+--RawGenomicSignals

Directly known subclasses: AbstractCNData, AbstractPSCNData, NonPairedPSCNData, PairedPSCNData, RawAlleleBFractions, RawCopyNumbers, RawMirroredAlleleBFractions, RawSequenceReads, SegmentedAlleleBFractions, SegmentedCopyNumbers

public class RawGenomicSignals extends RichDataFrame

Usage

RawGenomicSignals(y=NULL, x=NULL, w=NULL, chromosome=0L, name=NULL, ...)

Arguments

A numeric vector of length J specifying the signal at each locus.

A (optional) numeric vector of length J specifying the position of each locus.

A (optional) non-negative numeric vector of length J specifying a weight of each locus.

chromosome

An (optional) integer specifying the chromosome for these genomic signals.

name

An (optional) character string specifying the sample name.

...

Not used.

Fields and Methods

Methods:

	`*`
-
`+`	-
	`-`
-
`addBy`	-
	`append`
-
`as.data.frame`	-
	`binnedSmoothing`
-
`divideBy`	-
	`drawDensity`
-
`estimateStandardDeviation`	-
	`gaussianSmoothing`
-
`getChromosome`	-
	`getChromosomes`
-
`getPositions`	-
	`getSigma`
-
`getSignals`	-
	`getWeights`
-
`getXScale`	-
	`getYScale`
-
`hasWeights`	-
	`kernelSmoothing`
-
`lines`	-
	`multiplyBy`
-
`nbrOfChromosomes`	-
	`nbrOfLoci`
-
`plot`	-
	`points`
-
`segmentByCBS`	-
	`segmentByGLAD`
-
`segmentByHaarSeg`	-
	`segmentByMPCBS`
-
`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