I think I have a very easy question but unfortunately I haven't found a good answer yet, it's basically that I would like to annotate, using R, illumina epic probe sites according to their location, We did an experiment using Illumina Epic probes, and I now have my matrix of average beta values differences between two conditions for each probe, and I am trying to create a graph such as (E) and (F) here, where the Y axis is the average beta value difference for the probe and the X-axis corresponds to the location of this probe (transcription factor binding site, open chromatin, DNase I hypersensitive sites, etc). For this I need to annotate the probes, how can I do that?
I've been looking at the IlluminaMethylationManifest but it is not clear at all how to use it for this.
Any suggestions appreciated.
Just in case, check if you're using EPIC v1 and EPIC v2, because the annotations are different (see this and this packages)
Thanks, I am using EPIC v2, yet, it is not clear to me how to get right information from the manifest.
If you install and load these packages, you can get a data.frame within R with the information of probe names, coordinates, genes mapped to, etc., as such: