plotMethMap {BiSeq} | R Documentation

## Plots methylation values of multiple samples in a given region

### Description

A heatmap like plot is generated showing the relative methylation of single CpG sites. Samples are clustered hierarchically.

### Usage

    plotMethMap(object, region, groups, intervals, ...)

### Arguments

`object` | A `BSraw` or `BSrel` object storing the methylation values.
`region` | A `GRanges` object giving the region of interest.
`groups` | OPTIONAL. A `factor` that will be encoded by a color bar.
`intervals` | OPTIONAL. A `logical` indicating whether neighboured CpG sites should be placed side by side (if `FALSE`) or whether the intervals between CpG sites should be preserved (if `TRUE`).
`...` | Further arguments passed to the `heatmap` function.

### Details

The relative methylation values are passed to the heatmap function. Default colors are green (not methylated), black and red (methylated). To ensure that a relative methylation of 0 corresponds to green, 0.5 to black and 1 to red, the default value for the `zlim` argument of the `heatmap` function is set to `c(0,1)`. And the default for the `scale` parameter is set to `"none"`.
If argument `intervals` is set to `TRUE`, region should not be too large (< 1kb) and respect the resolution of your screen.

### Author(s)

Hans-Ulrich Klein

### See Also

`heatmap`, `BSraw-class`, `BSrel-class`, `filterBySharedRegions`, `filterByCov`

### Examples

    data(rrbs)
    data(predictedMeth)
    data(DMRs)

    plotMethMap(rrbs, region = DMRs[4], groups = colData(rrbs)[, "group"])

    plotMethMap(predictedMeth, region = DMRs[4],
                groups = colData(rrbs)[,"group"], intervals = FALSE)

[Package BiSeq version 1.26.0 Index]