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.
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.
#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.