xps (version 1.32.0)

rleplot-methods: Box Plots of Relative Log Expression (RLE)

Description

Produce boxplots of Relative Log Expression (RLE) values for the set of arrays.

Usage

rleplot(x, which = "UnitName", size = 0, range = 0, names = "namepart", main = "RLE Plot", ylim = c(-1.0, 1.0), las = 2, add.line = TRUE, outline = FALSE, ...)

Arguments

x

object of class ExprTreeSet or QualTreeSet.

which

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

size

length of sequence to be generated as subset.

range

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

names

optional vector of sample names.

main

the main title for the plot.

ylim

range for the plotted y values.

las

the style of axis labels.

add.line

logical, if TRUE a horizontal line is drawn.

outline

if outline is not true, the outliers are not drawn.

...

optional arguments to be passed to boxplot.

Details

Create boxplots of Relative Log Expression (RLE) values for the set of arrays, i.e. of M plots, where M is determined relative to a pseudo-median reference chip.

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 boxplot.

If an object of class QualTreeSet was created by fitting a probe level model with qualopt="all" then rleplot will plot RLE for "all" quality options. If you want to plot RLE for a certain quality option only, e.g. "normalized" data only, then you can use parameter names with names="namepart:", e.g. names="namepart:normalized".

See Also

RLE, plotRLE, mboxplot, nuseplot

Examples

# load existing ROOT scheme file and ROOT expression file for rma
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.rma <- root.expr(scheme.test3, paste(path.package("xps"),"rootdata/tmp_Test3RMA.root",sep="/"), "mdp")

if (interactive()) {
rleplot(data.rma)
}