densityBeanPlot: Density bean plots of methylation Beta values.
In minfi: Analyze Illumina Infinium DNA methylation arrays

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2	densityBeanPlot(dat, sampGroups = NULL, sampNames = NULL, main = NULL, pal = brewer.pal(8, "Dark2"), numPositions = 10000)

`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.

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.

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

Martin Aryee aryee@jhu.edu.

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

qcReport, mdsPlot, controlStripPlot, densityPlot

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)

}