plot_annotate_region {DMRforPairs} | R Documentation

## PLOT METHYLATION AND ANNOTATE REGION

### Description

Wrapper for `plot_annotate_probes`. Generates a plot of the methylation status of a region identified by DMRforPairs and associated transcripts (if annotate=TRUE).

### Usage

    plot_annotate_region(tested,regions,margin=10000,regionID,clr=NA,annotate=TRUE,scores=TRUE, path)

### Arguments

`tested` | Output of `testregion`
`regions` | Output of `regionfinder`
`margin` | See `export_data`
`regionID` | ID of a region identified by DMRforPairs as presented in the output of `testregion` and the output generated by `export_data`.
`clr` | See `export_data`
`annotate` | If FALSE, only basic visualizations without annotation information are generated. (default=TRUE)
`scores` | Specifies if statistics need to be calculated for the region or just figures. In a custom request from a user, statistics are relevant to calculate. In the `export_data` wrapper, they are redundant (already calculated in the `testregion` loop). (default=TRUE)
`path` | Path relative to the 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 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`, `testregion`.

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

    plot_annotate_region(example_output_DMRforPairs$tested,
                         example_output_DMRforPairs$regions,
                         margin=10000,
                         regionID=7,
                         annotate=FALSE,scores=TRUE,path=experiment)

[Package DMRforPairs version 1.22.0 Index]