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Analyses of differentially methylated regions (DMRs)
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To detect regional differential methylation signals among the CpGs that passed screening, an R package DMRcate was used [64]. The default settings in DMRcate include having at least two CpGs in a region and a minimum length of 1000 nucleotides. In our study, a DMR was considered to be statistically significant if the false discovery rate (FDR)-adjusted p value was < 0.05 [64]. Since DMR analyses focus on contribution of a region as a whole unit, a significant DMR can be detected even if there is no genome-wide significant individual CpGs in the region.
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