plotBetasByType {minfi} | 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.

### See Also

`densityPlot`, `densityBeanPlot`, `par`, `legend`

### 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)

[Package minfi version 1.34.0 Index]