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===Question: which metric of methylation variability should be used?=== * Coefficient of variation - standard deviation / mean = high values for low mean. This may not be altogether bad, since low mean could means that there are mostly unmethylated tissues and few methylated tissues. High CV regions are highly enriched for DHS and TFBS. * Standard deviation - too variable? * Maximum absolute pairwise distance - definitely show which region have tissue variable methylation when this value is high * Solution: utilize a combination of high coefficient of variation and high maximum absolute pairwise distance to identify a set of high methylation variable sites. * After filtering out sites categorized as high coefficient of variation and high maximum absolute pairwise distance - 2,562,875 CpG sites (10.6% out of 24,224,775 included in the segmentation) * Combined sites within 100 bp of each other into one region - 646,294 regions * 646,294 regions Minimum size: 1 bp, Median size: 38 bp, Mean size: 92.85 bp, Max size: 4,544 bp * I filtered out sites within the 95% percentile of the low or middle segmented states: 95%-tile of max absolute distance : 0.339 95%-tile of coefficient of variation: 0.142412 Remaining tissue specific CpGs : 2,557,584 * Combined sites within 100 bp of each other into one region - 644,917
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