plotMeth {segmentSeq} | R Documentation

## Plots a map of cytosine methylation (and optionally, methylation loci).

### Description

This function takes an `alignmentMeth` object and plots the observed levels of methylation within some defined region on the genome. If a `methData` object is also supplied, loci of methylation will also be shown.

### Usage

    plotMeth(aM, loci, chr, limits, samples, showNumber = TRUE, rgb = c(1, 0, 0), angle = 45, cap, add = FALSE)

### Arguments

`aM` | An `alignmentMeth`.
`loci` |
`chr` | The name of the chromosome to be plotted. Should correspond to a chromosome name in the `alignmentMeth` object.
`limits` | The start and end point of the region to be plotted.
`samples` | The sample numbers of the samples to be plotted. If NULL, plots all samples.
`showNumber` | Should the row number of each segment be shown?
`rgb` | The rgb code (`rgb`) with which to colour the loci.
`angle` | The angle at which loci are shaded (see `rect`).
`cap` | Caps the maximum level of coverage shown on the plot; thus, if a base has been sequenced at a level greater than the cap, the data for that base will be shown as if it has a coverage of cap.
`add` | If TRUE, adds the plot of methylation level to the current plot. Defaults to FALSE.

### Value

Plotting function.

### Author(s)

Thomas J. Hardcastle

### See Also

`alignmentMeth`

[Package segmentSeq version 2.18.0 Index]