plot_annotate_probes {DMRforPairs} | R Documentation

## PLOT METHYLATION+ANNOTATE A SET OF PROBES

### Description

Function that visualizes the methylation status of a selection of adjacent probes and (if requested) identifies transcripts associated with that region. If n>2 plots are generated for all samples together as well as in a pairwise fashion.

### Usage

    plot_annotate_probes(regions,title_x,probe_rows,margin=10000,ID=NA,clr=NA,annotate=TRUE,scores=NA,path)

### Arguments

`regions` | See output of `regionfinder`.
`title_x` | String which will be used as the main title of the scatter plots of the beta and M values.
`probe_rows` | Row numbers of the adjacent probes of interest in the regions object. See output of `regionfinder`:$perprobe, $valid.probes, $valid.m, $valid.beta.
`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`
`scores` | see `plot_annotate_region`
`path` | Path relative to the current working directory to save the files (=experiment.name in `export_data`)

### Details

A plot will be generated using only probes present in the DMRforPairs output (i.e. associated to one or more of the recoded classes, see `merge_classes`). This function is rarely called directly by the user. There are a number of wrappers available which lookup the probes (probe_rows) associated with a regionID from DMRforPairs, a custom genomic region or a gene of interest and then call plot_annotate_probes().

### Value

A number of figures (including pairwise plots if n>2) is generated visualizing methylation status in the samples at / near the probes 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_region`, `regionfinder`, `merge_classes`.

### Examples

    #This function is called by the other plot_annotate_...() wrappers and is
    #not usually called by the user directly.
    #Please see these functions for examples.

[Package DMRforPairs version 1.30.0 Index]