minfi (version 1.18.4)

densityBeanPlot: Density bean plots of methylation Beta values.

Description

Density ‘bean’ plots of methylation Beta values, primarily for QC.

Usage

densityBeanPlot(dat, sampGroups = NULL, sampNames = NULL, main = NULL, pal = brewer.pal(8, "Dark2"), numPositions = 10000)

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.

sampNames

Optional sample names. See details.

main

Plot title.

pal

Color palette.

numPositions

The density calculation uses numPositions randomly selected CpG positions. If NULL use all positions.

Value

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

Details

This function produces the density bean plot component of the QC report. If sampGroups is specified, group-specific colors will be used. For speed reasons the plots are produced using a random subset of CpG positions. The number of positions used is specified by the numPositions option.

References

P Kampstra. Beanplot: A boxplot alternative for visual comparison of distributions. Journal of Statistical Software 28, (2008). http://www.jstatsoft.org/v28/c01

See Also

qcReport, mdsPlot, controlStripPlot, densityPlot

Examples

if (require(minfiData)) {

names <- pData(RGsetEx)$Sample_Name
groups <- pData(RGsetEx)$Sample_Group
par(mar=c(5,6,4,2))
densityBeanPlot(RGsetEx, sampNames=names, sampGroups=groups)

}