densityPlot: Density plots of methylation Beta values.

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

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 [e-mail].

See Also

qcReport, mdsPlot, controlStripPlot, densityBeanPlot

Examples

if (require(minfiData)) {

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

}

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.