rnb.plot.locus.profile {RnBeads} | R Documentation

## rnb.plot.locus.profile

### Description

Computes methylation distributions for various region types and sample groups

### Usage

    rnb.plot.locus.profile(rnbSet, chrom, start, end, grps = NULL,
      plot.m.regions = NULL, plot.m.heatmap = TRUE, plot.m.smooth = TRUE,
      cvals.grps = rnb.getOption("colors.category"),
      cvals.meth = rnb.getOption("colors.meth"), smooth.profile = "wide")

### Arguments

`rnbSet` | RnBSet object
`chrom` | chromosome of window to plot
`start` | start coordinate of window to plot
`end` | end coordinate of window to plot
`grps` | a list of indices for each group to be compared or NULL if no sample grouping information should be displayed
`plot.m.regions` | character vector of region types whose methylation values should be displayed If `grps` is not `NULL` the methylation values will be separated by sample groups.
`plot.m.heatmap` | flag indicating whether sites methylation values should be displayed in a heatmap. If `grps` is not `NULL` the heatmaps will be separated by sample groups.
`plot.m.smooth` | flag indicating whether a scatterplot with smoothing curves should be displayed. If `grps` is not `NULL` the colors will be used to separate sample groups.
`cvals.grps` | colors to be used for the different groups
`cvals.meth` | colors to be used for methylation values and heatmaps
`smooth.profile` | profile to be used for the smoothing curves. Allowed values include `wide` (default) which yields smoother curvers and `narrow` which yields more "wiggly" curves

### Value

a `ggplot2` plot object containing the plot

### Author(s)

Fabian Mueller

### Examples

    #see RnBeads vignette (section: 'Generating Locus Profile Plots') for examples

[Package RnBeads version 1.12.1 Index]