AbstractCNData: The AbstractCNData class

Description

Package: aroma.core Class AbstractCNData

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

Directly known subclasses: AbstractPSCNData, NonPairedPSCNData, PairedPSCNData

public class AbstractCNData extends RawGenomicSignals

An AbstractCNData object holds copy number data.

Usage

AbstractCNData(chromosome=NULL, x=NULL, y=NULL, ..., name=NULL, .virtuals=NULL)

Arguments

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.

Optional numeric vector of J genomic locations. If NULL, index locations 1:J are used.

Optional numeric vector of J genomic locations.

...

Optional named locus-specific signal vectors of length J.

name

Optional character string.

.virtuals

(Internal) a list with virtual column name functions.

Fields and Methods

Methods:

	`findLargeGaps`	-
	`getChipType`	-
	`getLocusData`	-
	`getPlatform`	-
	`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: $, $<-, 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, 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