pmplot-methods: Barplot of PM and MM Intensities.

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.

Usage

pmplot(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", ...)

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.
...	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.

Note

Data must first be attached to class DataTreeSet using method attachInten.

Author(s)

Christian Stratowa

See Also

plotPM, boxplot, barplot

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 scheme mask and probe intensities
data.test3 <- attachMask(data.test3)
data.test3 <- attachInten(data.test3)

if (interactive()) {
pmplot(data.test3)
}

## optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)

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