RawGenomicSignals {aroma.core}R Documentation

The RawGenomicSignals class


Package: aroma.core
Class RawGenomicSignals


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

public class RawGenomicSignals
extends RichDataFrame


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



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.


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


An (optional) character string specifying the sample name.


Not used.

Fields and 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, 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


Henrik Bengtsson

[Package aroma.core version 3.2.2 Index]