From: De novo identification of differentially methylated regions in the human genome
Method | Implementationlanguage | Relevant parameters used in call a | Computational time (to nearest second) b |
---|---|---|---|
DMRcate v1.2.0 | R | lambda = 1000, C=2, p.adjust.method = ~BH~, pcutoff = α | 129 |
Bumphunter from minfi v1.10.2 | R | cluster = NULL, maxGap = 1000, smooth = TRUE, smoothFunction = loessByCluster, cutoff = α | 58 |
comb-p v0.35 | Python | –dist 1000 –seed α | 96 |
Probe Lasso from ChAMP v1.2.7 | R | filterXY = F, mafPol.lower = 0, mafPol.upper = 1, lassoRadius = 1000, minDmrSep = 1000, adjPVal = 1, minSigProbesLasso = 1, DMRpval = α | 6,867 |