densityBeanPlot {minfi} | R Documentation

## 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 aryee@jhu.edu.

### 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)

    }

[Package minfi version 1.28.4 Index]