I need to work with methylation data. GDC provides a vast dataset of methylation-array samples.
I noticed that for all the probes, they associate one or more ENSEMBL transcript ID.
My (most probably stupid) question is: are these data a sort of "Whole Exome Sequencing" rather than a "Whole Genome Sequencing"? I mean, does GDC for any reason provide only information about the exome, similarly to what they do for somatic mutations?