plot_annotate_gene {DMRforPairs} | R Documentation

## PLOT METHYLATION VALUES AROUND A GENE

### Description

Wrapper for `plot_annotate_probes`. Generates a plot of the methylation status of / around a specific gene.

### Usage

    plot_annotate_gene(gs,regions,margin=10000,ID,clr=NA,annotate=TRUE,path)

### Arguments

`gs` | Gene Symbol of interest
`regions` | Output of `regionfinder`
`margin` | See `export_data`
`ID` | Custom string which will be used as the file name of the figures generated
`clr` | See `export_data`
`annotate` | See `plot_annotate_region`
`path` | Path relative to the current working directory to save the files (=experiment.name in `export_data`)

### Details

Expects a subfolder with the name of your experiment to exist as created by export_data(). Writing permissions are required in the working directory to use the export and visualization functions of DMRforPairs. 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 gene 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"

    plot_annotate_gene(gs="DUS4L",
                       regions=example_output_DMRforPairs$regions,
                       margin=10000,
                       ID="DUS4L",
                       annotate=FALSE,path=experiment)

[Package DMRforPairs version 1.22.0 Index]