RawCopyNumbers: The RawCopyNumbers class

In aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

The RawCopyNumbers class

Description

Package: aroma.core
Class RawCopyNumbers

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

Directly known subclasses:
SegmentedCopyNumbers

public class RawCopyNumbers
extends RawGenomicSignals

Usage

RawCopyNumbers(cn=NULL, ...)

Arguments

cn	A numeric vector of length J specifying the copy number at each loci.
...	Arguments passed to RawGenomicSignals.

Fields and Methods

Methods:

	cnRange	-
	extractRawCopyNumbers	-
	getSignals	-
	plot	-

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:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Simulating copy-number data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Number of loci
J <- 1000

mu <- double(J)
mu[200:300] <- mu[200:300] + 1
mu[650:800] <- mu[650:800] - 1
eps <- rnorm(J, sd=1/2)
y <- mu + eps
x <- sort(runif(length(y), max=length(y)))


cn <- RawCopyNumbers(y, x)
print(cn)

cn2 <- extractSubset(cn, subset=xSeq(cn, by=5))
print(cn2)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Plot along genome
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, ylim=c(-3,3))
title(main="Complete and subsetted loci")
points(cn2, col="red", pch=176, cex=2)

legend("topright", pch=c(19,176), col=c("#999999", "red"),
       sprintf(c("raw [n=%d]", "every 5th [n=%d]"),
               c(nbrOfLoci(cn), nbrOfLoci(cn2))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Binned smoothing
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Binned smoothing")

cnSa <- binnedSmoothing(cn, by=3)
lines(cnSa, col="blue")
points(cnSa, col="blue")

cnSb <- binnedSmoothing(cn, by=9)
lines(cnSb, col="red")
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "Bin(w=3) [n=%d]", "Bin(w=9) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Binned smoothing (by count)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Binned smoothing (by count)")

cnSa <- binnedSmoothing(cn, by=3, byCount=TRUE)
lines(cnSa, col="blue")
points(cnSa, col="blue")

cnSb <- binnedSmoothing(cn, by=9, byCount=TRUE)
lines(cnSb, col="red")
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "BinO(w=3) [n=%d]", "BinO(w=9) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Kernel smoothing (default is Gaussian)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Kernel smoothing w/ Gaussian kernel")

cnSa <- kernelSmoothing(cn, h=2)
points(cnSa, col="blue")

cnSb <- kernelSmoothing(cn, h=5)
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "N(.,sd=2) [n=%d]", "N(.,sd=5) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Kernel smoothing
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plot(cn, col="#999999", ylim=c(-3,3))
title(main="Kernel smoothing w/ uniform kernel")

xOut <- xSeq(cn, by=10)
cnSa <- kernelSmoothing(cn, xOut=xOut, kernel="uniform", h=2)
lines(cnSa, col="blue")
points(cnSa, col="blue")

cnSb <- kernelSmoothing(cn, xOut=xOut, kernel="uniform", h=5)
lines(cnSb, col="red")
points(cnSb, col="red")

legend("topright", pch=19, col=c("#999999", "blue", "red"),
       sprintf(c("raw [n=%d]", "U(w=2) [n=%d]", "U(w=5) [n=%d]"),
       c(nbrOfLoci(cn), nbrOfLoci(cnSa), nbrOfLoci(cnSb))), bty="n")

aroma.core documentation built on Nov. 16, 2022, 1:07 a.m.