plot_annotate_probes: PLOT METHYLATION+ANNOTATE A SET OF PROBES

In DMRforPairs: DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

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, [e-mail]

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.  

DMRforPairs documentation built on Nov. 8, 2020, 4:52 p.m.