RawGenomicSignals {aroma.core}R Documentation

The RawGenomicSignals class

Description

Package: aroma.core
Class RawGenomicSignals

Object
~~|
~~+--RawGenomicSignals

Directly known subclasses:
RawAlleleBFractions, RawCopyNumbers, RawMirroredAlleleBFractions, RawSequenceReads, SegmentedAlleleBFractions, SegmentedCopyNumbers

public static class RawGenomicSignals
extends Object

Usage

RawGenomicSignals(y=NULL, x=NULL, w=NULL, chromosome=NA, 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) @characte string specifying the sample name.
... Not used.

Fields and Methods

Methods:
addBy -
addLocusFields -
append -
as.data.frame -
binnedSmoothing -
divideBy -
estimateStandardDeviation Estimates the standard deviation of the raw Ys.
extractRegion -
extractSubset -
gaussianSmoothing -
getChromosome -
getLocusFields -
getName -
getPositions -
getSigma -
getSignals -
getWeights -
getXScale -
getXY -
getYScale -
hasWeights -
kernelSmoothing -
lines -
multiplyBy -
nbrOfLoci -
plot -
points -
setLocusFields -
setSigma -
setWeights -
setXScale -
setYScale -
signalRange -
sort -
subtractBy -
summary -
xMax -
xMin -
xRange -
xSeq -
yMax -
yMin -
yRange -

Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)


[Package aroma.core version 1.2.0 Index]