xps (version 1.32.0)

mboxplot-methods: Box Plots of Relative M Values

Description

Produce boxplots of relative M values for the set of arrays.

Usage

mboxplot(x, which = "", size = 0, transfo = log2, method = "mean", range = 0, ylim = c(-1,1), outline = FALSE, names = "namepart", ...)

Arguments

x

object of class DataTreeSet or ExprTreeSet.

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 create the reference data, “mean” or “median”.

range

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

ylim

range for the plotted y values.

outline

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

names

optional vector of sample names.

...

optional arguments to be passed to boxplot.

Details

Create boxplots of M plots, where M is determined relative to a pseudo-mean 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.

See Also

mvaplot, boxplot

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()) {
mboxplot(data.test3, ylim=c(-6,6))
}

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