RawGenomicSignals: The RawGenomicSignals class

In aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

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

y	A numeric vector of length J specifying the signal at each locus.
x	A (optional) numeric vector of length J specifying the position of each locus.
w	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:
$<-,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, as.vector, 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, xtfrm

Author(s)

Henrik Bengtsson

aroma.core documentation built on June 25, 2024, 1:15 a.m.