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) character 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 -
setName -
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 1.4.0 Index]