Fig. 2

Defiant uses WWE for DMR identification. We used artificial data designed for Metilene [27]. Each group is composed of ten replicate DNA methylation samples. The top two panels show the level of DNA methylation for each CpG (box-and-whisker plots). The mean is weighted based on coverage. The third panel from the top shows the weighted Welch p-value between the sets for individual CpG. The bottom panel shows differences between the weighted mean. Defiant calls a DMR when it finds consecutive CpGs with 1) differences in methylation levels, 2) minimum coverage, 3) p-value. When Defiant finds consecutive CpGs that do not match the above criteria, the expansion of a DMR stops. The third and fourth panels show the DMR start and end points in red