DNA methylation EPIC array and ChromHMM
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!
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