xps (version 1.32.0)

intensity2GCplot-methods: Boxlot of Probe Intensities Stratified by GC Content.

Description

Creates a boxplot of probe intensities stratified by GC content.

Usage

intensity2GCplot(x, treename, which = "", transfo = log2, range = 0, col = c("lightblue", "darkblue"), ...)

Arguments

x

object of class DataTreeSet.

treename

character vector, tree name containing intensities.

which

type of probes to be used, for details see validData.

transfo

a valid function to transform the data, usually “log2”, or “0”.

range

determines how far the plot whiskers extend out from the box.

col

color pair to be used by function colorRampPalette.

...

optional arguments to be passed to intensity2GCplot.

Details

Creates a boxplot of probe intensities for treename stratified by GC content for an object of class DataTreeSet.

See Also

plotIntensity2GC

Examples

## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## need to attach probe G/C content and optionally mask
data.test3 <- attachProbeContentGC(data.test3)
data.test3 <- attachMask(data.test3)

if (interactive()) {
intensity2GCplot(data.test3, treename = "TestA1.cel", which="mm")
}

## optionally remove probe G/C content and mask to free memory
data.test3 <- removeMask(data.test3)
data.test3 <- removeProbeContentGC(data.test3)