minfi (version 1.18.4)

densityPlot: Density plots of methylation Beta values.

Description

Density plots of methylation Beta values, primarily for QC.

Usage

densityPlot(dat, sampGroups = NULL, main = "", xlab = "Beta", pal = brewer.pal(8, "Dark2"), xlim, ylim, add = TRUE, legend = TRUE, ...)

Arguments

dat

An RGChannelSet, a MethylSet or a matrix. We either use the getBeta function to get Beta values (for the first two) or we assume the matrix contains Beta values.

sampGroups

Optional sample group labels. See details.

main

Plot title.

xlab

x-axis label.

pal

Color palette.

xlim

x-axis limits.

ylim

y-axis limits.

add

Start a new plot?

legend

Plot legend.

...

Additional options to be passed to the plot command.

Value

No return value. Plots are produced as a side-effect.

Details

This function produces the density plot component of the QC report. If sampGroups is specified, group-specific colors will be used.

See Also

qcReport, mdsPlot, controlStripPlot, densityBeanPlot

Examples

if (require(minfiData)) {

groups <- pData(RGsetEx)$Sample_Group
densityPlot(RGsetEx, sampGroups=groups)

}