plotIntensity2GC: Boxlot of Probe Intensities Stratified by GC Content for...

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 for the selected device.

Usage

plotIntensity2GC(x,
                 treename, 
                 which   = "",
                 transfo = log2,
                 range   = 0,
                 col     = c("lightblue", "darkblue"),
                 dev     = "screen",
                 outfile = "Intensity2GCPlot",
                 w       = 540,
                 h       = 540,
                 ...) 

Arguments

x	object of class DataTreeSet.
treename	character vector, tree name used for 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.
dev	graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.
outfile	the name of the output file.
w	the width of the device in pixels.
h	the height of the device in pixels.
...	optional arguments to be passed to plotIntensity2GC.

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

intensity2GCplot

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