RawGenomicSignals: The RawGenomicSignals class
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. Fields and Methods
Methods:
rll{
- -
* -
+ -
addBy -
addLocusFields -
append -
as.data.frame -
binnedSmoothing -
divideBy -
drawDensity -
estimateStandardDeviation Estimates the standard deviation of the raw Ys.
extractRegion -
extractRegions -
extractSubset -
gaussianSmoothing -
getChromosome -
getLocusFields -
getName -
getPositions -
getSigma -
getSignals -
getWeights -
getXScale -
getXY -
getYScale -
hasWeights -
kernelSmoothing -
lines -
multiplyBy -
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.
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