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Table 1 Overview and guidance on common and selected R packages used in DNA methylation pipelines as a starting point for making decisions based on the desired estimate. See Heiss et al. [4] for information on the differences between Illumina microarrays and bisulfite sequencing. See table 3 for information on M-values and Beta-values

From: Estimands in epigenome-wide association studies

R function (Package) Estimates come from Used input
Full pipeline (DMCs and DMRs)
BioMethyl\(^1\)   M-values, Beta-values (BS-seq\(^{\dagger }\))
minfi\(^{2}\)   M-values, Beta-values
ChAMP\(^{3}\)   M-values, Beta-values
RnBeads\(^{4}\)   M-values (BS-seq\(^{\dagger }\))
metilene\(^{5}\)   Beta-values (BS-seq\(^{\dagger }\))
Preprocessing\(^{\ddagger }\)
ComBat (sva\(^6\))   M-values (BS-seq\(^{\dagger }\))
melon (wateRmelon\(^{7}\))   Beta-values
BMIQ (wateRmelon\(^{7}\))   Beta-values
SWAN (missMethyl\(^{8}\))   Beta-values
CellDMC (EpiDISH\(^9\)) lm (stats) Beta-values
Detect differentially methylated single CpG sites (DMCs)
champ.DMP (ChAMP\(^3\)) lmFit (limma\(^{10}\)) M-values, Beta-values
dmpFinder (minfi\(^2\)) lmFit (limma\(^{10}\)) M-values, Beta-values
calDEG (BioMethyl\(^1\)) t-test M-values, Beta-values
varFit (missMethyl\(^{8}\)) lmFit (limma\(^{10}\)) M-values
DMLtest (DSS\(^{11}\))   Count values (BS-seq\(^{\dagger }\))
Detect differentially methylated regions (DMRs)
bumphunter (bumphunter\(^{12}\)) lmFit (limma\(^{10}\)) M-values(BS-seq\(^{\dagger }\), after transformation)
champ.DMR (ChAMP\(^3\)) bumphunter (bumphunter\(^{12}\)) M-values
dmrcate (DMRcate\(^{13}\)) lmFit (limma\(^5\)) M-values (BS-seq\(^{\dagger }\))
gometh (missMethyl\(^{8}\))   M-values, Beta-values
BSmooth (bsseq\(^{14}\))   Beta-values (BS-seq\(^{\dagger }\))
  1. \(^1\)Wang [59], \(^2\)Aryee [32], \(^3\)Tian [31], \(^{4}\)Müller [29], \(^{5}\)Jühling [36],
  2. \(^6\)Johnson [52], \(^{7}\)Pidsley [44], \(^{8}\)Phipson [60], \(^9\)Zheng [35], \(^{10}\)Smyth [34],
  3. \(^{11}\)Park [16] \(^{12}\)Irizarry [61], \(^{13}\)Peters [62], \(^{14}\)Hansen [63]
  4. \(^{\dagger }\)BS-seq: Supports (processed) bisulfite sequencing data. Packages might need “transformed count data”
  5. \(^{\ddagger }\)See Assenov [30] for bisulfite sequencing and McEwen [33] for Illumina microarray data