plotBetasByType: Plot the overall distribution of beta values and the...
In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

plotBetasByType

R Documentation

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.

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.

Value

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

Author(s)

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

Examples

## Not run: 
if (require(minfiData)) {
  Mset.swan <- preprocessSWAN(RGsetEx, MsetEx)
  par(mfrow=c(1,2))
  plotBetasByType(MsetEx[,1], main="Raw")
  plotBetasByType(Mset.swan[,1], main="SWAN")
}

## End(Not run)

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