densityBeanPlot: Density bean plots of methylation Beta values.

In kasperdanielhansen/minfi: Analyze Illumina Infinium DNA methylation arrays

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.

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.

Value

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

Author(s)

Martin Aryee [e-mail].

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)

}

kasperdanielhansen/minfi documentation built on Jan. 13, 2024, 9:30 p.m.