aroma.core (version 2.9.0)

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=0, 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: rll{ * - + - - - addBy - append - as.data.frame - binnedSmoothing - divideBy - drawDensity - estimateStandardDeviation Estimates the standard deviation of the raw Ys. gaussianSmoothing - getChromosome - getChromosomes - getPositions - getSigma - getSignals - getWeights - getXScale - getYScale - hasWeights - kernelSmoothing - lines - multiplyBy - nbrOfChromosomes - nbrOfLoci - plot - points - segmentByCBS Segment copy numbers using the CBS method. segmentByGLAD Segment copy numbers using the GLAD method. segmentByHaarSeg Segment copy numbers using the HaarSeg method. segmentByMPCBS Segment copy numbers using the multi-platform CBS (mpCBS) method. 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, cbind, dim, dimnames, dimnames<-, droplevels, duplicated, edit, format, formula, head, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, split, split<-, stack, str, subset, summary, t, tail, transform, unique, unstack, unwrap, within, wrap, writeDataFrame