densityByProbeType: Plot the beta value distributions of the Infinium I and II...
In ChuanJ/test: Analysing Illumina HumanMethylation BeadChip Data

Description Usage Arguments Details Author(s) References See Also Examples

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

1 2	densityByProbeType(data, legendPos = "top", colors = c("black", "red", "blue"), main = "", lwd = 3, cex.legend = 1)

`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.
`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.

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 SWAN affects the data.

Jovana Maksimovic jovana.maksimovic@mcri.edu.au.

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

densityPlot, densityBeanPlot, par, legend

if (require(minfi) & require(minfiData)) {
  dat <- preprocessRaw(RGsetEx)
  datSwan <- SWAN(dat)
  par(mfrow=c(1,2))
  densityByProbeType(dat[,1], main="Raw")
  densityByProbeType(datSwan[,1], main="SWAN")
}