plotPM: Barplot of PM and MM Intensities for Device

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

Description

Creates a barplot of mean perfect match and mismatch intensities for the selected device.

Usage

plotPM(x,
       which   = "",
       size    = 0,
       transfo = NULL,
       method  = mean,
       names   = "namepart",
       beside  = TRUE,
       col     = c("red", "blue"),
       legend  = c("PM","MM"),
       las     = 2,
       ylab    = "mean intensities",
       dev     = "screen",
       outfile = "PMPlot",
       w       = 540,
       h       = 540,
       ...) 

Arguments

x	object of class DataTreeSet.
which	type of probes to be used, for details see validData.
size	length of sequence to be generated as subset.
transfo	a valid function to transform the data, usually “log2”, or “0”.
method	method to compute average intensities, “mean” or “median”.
names	optional vector of sample names.
beside	logical. If FALSE, mean intensities are portrayed as stacked bars, and if TRUE the columns are portrayed as juxtaposed bars.
col	color of PM, MM bars.
legend	a vector of text used to construct a legend for the plot, or a logical indicating whether a legend should be included.
las	the style of axis labels.
ylab	a title for the y axis.
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 barplot.

Details

Produces barplots of mean perfect match and mismatch intensities for slot data for an object of class DataTreeSet.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as pmplot.

Author(s)

Christian Stratowa

See Also

pmplot

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