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aroma.core (version 2.2.0)

RawSequenceReads: The RawSequenceReads class

Description

Package: aroma.core Class RawSequenceReads Object ~~| ~~+--RawGenomicSignals ~~~~~~~| ~~~~~~~+--RawSequenceReads Directly known subclasses: public static class RawSequenceReads extends RawGenomicSignals

Usage

RawSequenceReads(x=NULL, y=rep(1, length(x)), ...)

Arguments

x
An integer vector of length J specifying the read positions.
y
An (optional) integer vector of length J specifying the number of reads at each position. Default is one read per position.
...
Arguments passed to RawGenomicSignals.

Fields and Methods

Methods: rll{ binnedSums - extractRawCopyNumbers - nbrOfReads - plot - } Methods inherited from RawGenomicSignals: -, *, +, addBy, addLocusFields, append, applyBinaryOperator, as.data.frame, binnedSmoothing, divideBy, drawDensity, estimateStandardDeviation, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getChromosome, getLocusFields, getName, getPositions, getSigma, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfLoci, plot, points, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setLocusFields, setName, setSigma, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, summary, xMax, xMin, xRange, xSeq, yMax, yMin, yRange Methods inherited from Object: asThis, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save