densityByProbeType: Plot the beta value distributions of the Infinium I and II...

In Oshlack/missMethyl: Analysing Illumina HumanMethylation BeadChip Data

Plot the beta value distributions of the Infinium I and II probe types relative to the overall beta value distribution.

Description

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

Usage

densityByProbeType(
  data,
  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.
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.

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 SWAN affects the data.

Value

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

Author(s)

Jovana Maksimovic

See Also

densityPlot, densityBeanPlot, par, legend

Examples

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")
}

Oshlack/missMethyl documentation built on March 26, 2023, 1:50 p.m.