plotMethDistribution {segmentSeq} | R Documentation

## Plots the distribution of methylation on the genome.

### Description

Plots the distribution of methylation (as defined in an `alignmentMeth` object upon the genome.

### Usage

    plotMethDistribution(meth, samples, bw = 1e-3, subtract, chrs, centromeres,
    add = FALSE, col, ylim = NULL, legend = TRUE, ...)

### Arguments

`meth` | An object of class `alignmentMeth` containing the methylation data.
`samples` | A numeric vector defining the columns of data in the ‘meth’ object from which to estimate proportions of methylation, or a list object containing numeric vectors if multiple distributions are to be derived from the ‘meth’ object, or a factor in which each level of the factor defines a set of columns for the ‘meth’ object. If missing, derived from the ‘@replicates’ slot of the ‘meth’ object.
`bw` | Gives the bandwidth of the density plots; analagous to the ‘bw’ parameter in `density`.
`subtract` | A numeric vector giving values to be subtracted from the density of methylation. See Details.
`chrs` | The names of the chromosomes for which a distribution should be plotted. If mising, derived from the ‘@alignments’ slot of the ‘meth’ object.
`centromeres` | If given, a numeric vector defining the position of the centromeres on the chromosomes. These will be then be plotted.
`add` | Should the distribution curve be added to an existing plot? Defaults to FALSE.
`col` | A vector of colours to be used to plot the distributions. If missing, generated from `rainbow`.
`ylim` | Limits on the y-axis. Defaults to NULL, in which case limits are automatically set.
`legend` | Should a legend be added to the plot? Defaults to TRUE.
`...` | Any additional parameters to be passed to `plot`.

### Details

The function returns the density of methylation calculated. This can be used in further plots as the 'subtract' parameter, which allows one methylation profile to be subtracted from another.

### Value

An object of class `density` describing the plotted distribution.

### Author(s)

Thomas J. Hardcastle

### See Also

`alignmentMeth`

[Package segmentSeq version 2.16.0 Index]