plot_annotate_custom_region {DMRforPairs} | R Documentation |
Wrapper for plot_annotate_probes
. Generates a plot of the methylation status of a custom genomic region.
plot_annotate_custom_region(chr,st,ed,regions,margin=10000,ID="CustomRegion",clr=NA,annotate=TRUE,path)
chr |
Chromosome on which the custom region is located. Number/X/Y only (i.e. no 'chr' prefix. |
st |
Start position (bp) of the custom region |
ed |
End position (bp) of the custom region |
regions |
See output of |
margin |
See |
ID |
String which will be used as the file name of the figures generated. (default = "CustomRegion") |
clr |
See |
annotate |
|
path |
Path relative to the current working directory to store the files (=experiment.name in |
A plot will be generated using only the probes present in the DMRforPairs
output (i.e. associated to one or more of the recoded classes, see merge_classes
).
Expects a writable subfolder of the curent working directory (as created by export_data()). 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 custom 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
,
#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" #visualize a custom region on the genome plot_annotate_custom_region(chr=7, st=1.05E+8, ed=1.06E+8, example_output_DMRforPairs$regions, margin=500, ID="custom_region", annotate=FALSE,path=experiment)