plot_annotate_custom_region {DMRforPairs} | R Documentation

## PLOT METHYLATION OF A CUSTOM GENOMIC REGION

### Description

Wrapper for `plot_annotate_probes`. Generates a plot of the methylation status of a custom genomic region.

### Usage

    plot_annotate_custom_region(chr,st,ed,regions,margin=10000,ID="CustomRegion",clr=NA,annotate=TRUE,path)

### Arguments

`chr` | Chromosome on which the custom region is located. Number/X/Y only (i.e. no 'chr' prefix.
`st` | Start position (bp) of the custom region
`ed` | End position (bp) of the custom region
`regions` | See output of `regionfinder`
`margin` | See `export_data`
`ID` | String which will be used as the file name of the figures generated. (default = "CustomRegion")
`clr` | See `export_data`
`annotate` | See `plot_annotate_region`
`path` | Path relative to the current working directory to store the files (=experiment.name in `export_data`)

### Details

A plot will be generated using only the probes present in the `DMRforPairs` output (i.e. associated to one or more of the recoded classes, see `merge_classes`).
Expects a writable subfolder of the curent working directory (as created by export_data()). Internet access is required to use the annotation features.

### Value

A number of figures (including pairwise plots if n>2) is generated, visualizing methylation status in the samples at / near the custom region investigated. Statistics and optional annotation information are reported back by the function.

### Author(s)

Martin Rijlaarsdam, m.a.rijlaarsdam@gmail.com

### See Also

`export_data`, `plot_annotate_probes`, `regionfinder`,

### Examples

    #For the this step, please ensure that you have writing
    #permissions in your working directory. If any of the
    #annotate parameters is set to TRUE, an internet connection
    #is required.

    #This example expects a folder "example_DMRforPairs" to exist and
    #be writable in the current working directory.
    data(DMRforPairs_data)
    experiment="example_DMRforPairs"

    #visualize a custom region on the genome
    plot_annotate_custom_region(chr=7,
                                st=1.05E+8,
                                ed=1.06E+8,
                                example_output_DMRforPairs$regions,
                                margin=500,
                                ID="custom_region",
                                annotate=FALSE,path=experiment)

[Package DMRforPairs version 1.30.0 Index]