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Table 1 Usage of the four candidate methods in this study

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
  1. aArgument α indicates the tuned parameter for which sets of called DMRs were produced. Any omissions imply function defaults. bComputational time is for the VA vs SA comparison, which is the time needed to fit the whole 450K methylome (using parameters in the previous column) with a single core of a clean Dual Xeon eight-core E5-2650 compute node, using 64 GB of virtual memory.