I'm posting my question here again as you suggested.
I want to build a matrix summarizing methylation levels at CpGs resolution from RRBS data of ENCODE (only from tissues and primary cell, hg19 genome), so that I get the methylation level of every possible CpG covered by one sample (or more). and then download this matrix and save to a file.
what is the easiest way to do it in DeepBlue? in R environment would be the best.
Customer support service by UserEcho