minfi (version 1.18.2)

plotBetasByType: Plot the overall distribution of beta values and the distributions of the Infinium I and II probe types.

Description

Plot the overall density distribution of beta values and the density distributions of the Infinium I and II probe types.

Usage

plotBetasByType(data, probeTypes = NULL, legendPos = "top",
                colors = c("black", "red", "blue"),
                main = "", lwd = 3, cex.legend = 1)

Arguments

data

A MethylSet or a matrix or a vector. We either use the getBeta function to get Beta values (in the first case) or we assume the matrix or vector contains Beta values.

probeTypes

If data is a MethylSet this argument is not needed. Otherwise, a data.frame with a column 'Name' containing probe IDs and a column 'Type' containing their corresponding assay design type.

legendPos

The x and y co-ordinates to be used to position the legend. They can be specified by keyword or in any way which is accepted by xy.coords. See legend for details.

colors

Colors to be used for the different beta value density distributions. Must be a vector of length 3.

main

Plot title.

lwd

The line width to be used for the different beta value density distributions.

cex.legend

The character expansion factor for the legend text.

Value

• No return value. Plot is produced as a side-effect.

Details

The density distribution of the beta values for a single sample is plotted. The density distributions of the Infinium I and II probes are then plotted individually, showing how they contribute to the overall distribution. This is useful for visualising how using preprocessSWAN affects the data.

See Also

densityPlot, densityBeanPlot, par, legend

Examples

if (require(minfiData)) {
  Mset.swan <- preprocessSWAN(RGsetEx, MsetEx)
  par(mfrow=c(1,2))
  plotBetasByType(MsetEx[,1], main="Raw")
  plotBetasByType(Mset.swan[,1], main="SWAN")
}