Workflow from Scientific Research

Differential methylation testing allows for a number of test choices. The LLR difference hypothesis compares methylation call LLRs within a segment between two samples directly. Selecting the count dependency hypothesis or the -score difference hypothesis (default) both result in binarization of methylation calls based on a defined LLR threshold. The count dependency hypothesis leads to a test on contingency tables, testing dependency between methylation count and read group, whereas the -score difference hypothesis results in a test comparing, for each segment, the read methylation rates between read groups. Regardless of test hypothesis, p -values are then subjected to multiple testing correction.

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