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

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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.

Note

G/C content must first be attached to class DataTreeSet using method attachProbeContentGC. It is also recommended to attach the probe mask using method attachMask.

Author(s)

Christian Stratowa

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)

xps documentation built on Nov. 8, 2020, 6 p.m.