I have DNA methylation data obtained by the EPIC array and I would like to use this data to check for chromatin states using the ChroHMM software. I understand that the data must be in a binary format, grouped by each 200bp, and separated by chromosome. I have been thinking and searching and I cannot come up with a solution on how to make my data binary and grouped each 200bp. Note that the whole chromosome is not sequenced by this technology, so i would have to group each 200 but regions without CpGs will need to receive a value of 2. Is there a package that can help me do that? Or has anyone done this before? Please any help would be appreciated!
Were you able to figure something out? Using EPIC data with chromHMM is something I am intererested in too, but can't find an the use of EPIC with chromHMM anywhere. Do you have any reference or papers that discuss using EPIC array to get chromatin states?
not yet. I got some papers that have done something similar but I haven't figured it out as yet.