PLOT METHYLATION+ANNOTATE A SET OF PROBES

Share:

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

1
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

1
2
3
#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.