rnb.plot.region.profiles {RnBeads} | R Documentation

## rnb.plot.region.profiles

### Description

Creates a composite plot showing the sample and groupwise smoothed estimates of methylation values accross all regions of the specified type

### Usage

    rnb.plot.region.profiles(rnb.set, group.index.list, region.type = "",
      region.profile = NULL, extend.by = 0.33,
      cvalues = rnb.getOption("colors.category"))

### Arguments

`rnb.set` | RnBSet object
`group.index.list` | a list (preferably named) containing sample indices for each group a list of such lists is for instance generated by the `rnb.sample.groups` function.
`region.type` | Region type for which the plot should be generated
`region.profile` | Alternative to specifying `region.type`, the function can accept a region profile generated by the `rnb.find.relative.site.coord` function
`extend.by` | A number between 0 and 1 specifying the percentage by which a region is extended in order to capture methylation information before region start and after region end
`cvalues` | Color values that will be assigned to sample groups

### Value

a ggplot2 object for plotting the plot shows the smoothed methylation levels of sites accross the specified region type for all regions of that type from 0 (region start) to 1 (region end). Sites in the flanking areas are also shown (coordinates <0 and >1). Smoothing is stratified by sample (dashed lines) and sample group (thick solid lines). Cubic splines are used for smoothing

### Author(s)

Fabian Mueller

### Examples

    #Careful: this might take a while
    library(RnBeads.hg19)
    data(small.example.object)
    logger.start(fname=NA)
    rnb.plot.region.profiles(rnb.set.example,rnb.sample.groups(rnb.set.example)[[1]],"genes")

[Package RnBeads version 1.12.1 Index]