plot_annotate_region {DMRforPairs} | R Documentation |
Wrapper for plot_annotate_probes
. Generates a plot of the methylation status of a region identified by DMRforPairs and associated transcripts (if annotate=TRUE).
plot_annotate_region(tested,regions,margin=10000,regionID,clr=NA,annotate=TRUE,scores=TRUE, path)
tested |
Output of |
regions |
Output of |
margin |
See |
regionID |
ID of a region identified by DMRforPairs as presented in the output of |
clr |
See |
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 |
path |
Path relative to the working directory to save the files (=experiment.name in |
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.
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.
Martin Rijlaarsdam, m.a.rijlaarsdam@gmail.com
export_data
,
plot_annotate_probes
,
regionfinder
,
testregion
.
#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)