Parameter settings for the DMR identification methods. Default settings are underlined and in bold font.
| Method . | Implementation . | Input Parameters . | Statistics for computing DMR P-value . | DMR P-value label in output table . |
|---|---|---|---|---|
| Bumphunter | R/BioC package bumphunter v1.20.0 | pickCutoffQ = (0.95, 0.99), maxGap = (200, 250, 500, 750, 1000), nullMethod ="permutation", B=10 | permutation distribution based on permuting sample labels | P-value area |
| Comb-p | Python library comb-p v0.48 | --seed (0.001, 0.01, 0.05) --dist (200, 250, 500, 750, 1000) | Stouffer–Liptak statistic | z_p |
| DMRcate | R/BioC package DMRcate v1.14.0 | lambda = (200, 250, 500, 750, 1000), C = (1,2,3,4,5) | Stouffer’s method | Stouffer |
| Probe Lasso | R/BioC package ChAMP v2.9.10 | method = “ProbeLasso”, adjPvalProbe = (0.001, 0.01, 0.05) meanLassoRadius = (375, 700, 1000) minDmrSep = (200, 250, 500, 750, 1000) | Stouffer’s method | dmrP |
| Method . | Implementation . | Input Parameters . | Statistics for computing DMR P-value . | DMR P-value label in output table . |
|---|---|---|---|---|
| Bumphunter | R/BioC package bumphunter v1.20.0 | pickCutoffQ = (0.95, 0.99), maxGap = (200, 250, 500, 750, 1000), nullMethod ="permutation", B=10 | permutation distribution based on permuting sample labels | P-value area |
| Comb-p | Python library comb-p v0.48 | --seed (0.001, 0.01, 0.05) --dist (200, 250, 500, 750, 1000) | Stouffer–Liptak statistic | z_p |
| DMRcate | R/BioC package DMRcate v1.14.0 | lambda = (200, 250, 500, 750, 1000), C = (1,2,3,4,5) | Stouffer’s method | Stouffer |
| Probe Lasso | R/BioC package ChAMP v2.9.10 | method = “ProbeLasso”, adjPvalProbe = (0.001, 0.01, 0.05) meanLassoRadius = (375, 700, 1000) minDmrSep = (200, 250, 500, 750, 1000) | Stouffer’s method | dmrP |
Parameter settings for the DMR identification methods. Default settings are underlined and in bold font.
| Method . | Implementation . | Input Parameters . | Statistics for computing DMR P-value . | DMR P-value label in output table . |
|---|---|---|---|---|
| Bumphunter | R/BioC package bumphunter v1.20.0 | pickCutoffQ = (0.95, 0.99), maxGap = (200, 250, 500, 750, 1000), nullMethod ="permutation", B=10 | permutation distribution based on permuting sample labels | P-value area |
| Comb-p | Python library comb-p v0.48 | --seed (0.001, 0.01, 0.05) --dist (200, 250, 500, 750, 1000) | Stouffer–Liptak statistic | z_p |
| DMRcate | R/BioC package DMRcate v1.14.0 | lambda = (200, 250, 500, 750, 1000), C = (1,2,3,4,5) | Stouffer’s method | Stouffer |
| Probe Lasso | R/BioC package ChAMP v2.9.10 | method = “ProbeLasso”, adjPvalProbe = (0.001, 0.01, 0.05) meanLassoRadius = (375, 700, 1000) minDmrSep = (200, 250, 500, 750, 1000) | Stouffer’s method | dmrP |
| Method . | Implementation . | Input Parameters . | Statistics for computing DMR P-value . | DMR P-value label in output table . |
|---|---|---|---|---|
| Bumphunter | R/BioC package bumphunter v1.20.0 | pickCutoffQ = (0.95, 0.99), maxGap = (200, 250, 500, 750, 1000), nullMethod ="permutation", B=10 | permutation distribution based on permuting sample labels | P-value area |
| Comb-p | Python library comb-p v0.48 | --seed (0.001, 0.01, 0.05) --dist (200, 250, 500, 750, 1000) | Stouffer–Liptak statistic | z_p |
| DMRcate | R/BioC package DMRcate v1.14.0 | lambda = (200, 250, 500, 750, 1000), C = (1,2,3,4,5) | Stouffer’s method | Stouffer |
| Probe Lasso | R/BioC package ChAMP v2.9.10 | method = “ProbeLasso”, adjPvalProbe = (0.001, 0.01, 0.05) meanLassoRadius = (375, 700, 1000) minDmrSep = (200, 250, 500, 750, 1000) | Stouffer’s method | dmrP |
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