Table 1 Comparison of differential methylation methods
| Â | DMRscaler | bumphunter | comb-p | DMRcate |
|---|---|---|---|---|
Individual CpG significance | NA (takes p-value as input) | t-test | NA (takes p-value as input) | -Â t-test, using M transformed Beta values |
DMRs definition | Iterative enrichment testing for significant CpGs within window | Consecutive CpGs above significance threshold | Groups significant CGs if within window or window interval | Gaussian smoothed regions above significance threshold |
DMR significance | Hypergeometric Test | Stouffer’s Method | Stouffer-Liptak | Permutation Test |
Parameters controlling size (default) | window_size (4,8,16,32,64 adj CpGs) | maxGap (500Â bp) | dist, step (no default) | lambda (1Â kb), C (2) |