plot_annotate_gene {DMRforPairs} | R Documentation |
Wrapper for plot_annotate_probes
. Generates a plot of the methylation status of / around a specific gene.
plot_annotate_gene(gs,regions,margin=10000,ID,clr=NA,annotate=TRUE,path)
gs |
Gene Symbol of interest |
regions |
Output of |
margin |
See |
ID |
Custom string which will be used as the file name of the figures generated |
clr |
See |
annotate |
|
path |
Path relative to the current 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 gene 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
,
#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 example expects a folder "example_DMRforPairs" to exist and #be writable in the current working directory. data(DMRforPairs_data) experiment="example_DMRforPairs" plot_annotate_gene(gs="DUS4L", regions=example_output_DMRforPairs$regions, margin=10000, ID="DUS4L", annotate=FALSE,path=experiment)