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

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

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

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.

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

Jovana Maksimovic

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")
}