densityPlot {minfi} | R Documentation

## 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.

### Details

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

### Value

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

### Author(s)

Martin Aryee aryee@jhu.edu.

### See Also

`qcReport`, `mdsPlot`, `controlStripPlot`, `densityBeanPlot`

### Examples

    if (require(minfiData)) {

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

    }

[Package minfi version 1.28.4 Index]