hist-methods {xps}R Documentation

Density Estimate

Description

Plot the density estimates for each sample.

Usage

hist(x, which = "", size = 0, transfo = log2, ylab = "density", xlab = "log intensity", type = "l", col = 1:6, ...)

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”.
ylab a title for the y axis.
xlab a title for the x axis.
type type for the plot.
col colors to use for the different arrays.
... optional arguments to be passed to plot.

Details

Plots the non-parametric density estimates using values contained in the columns of slot data.

For a DataTreeSet object, data must first be attached using method attachInten.

Note

For exon array raw data only a limited number of samples can be displayed as density plot due to memory limitations. To display all samples it is proposed to use function root.density instead.

Author(s)

Christian Stratowa

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()) {
hist(data.test3)
}

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

[Package xps version 1.2.10 Index]