differentialMethylation: Differential methylation analysis.
In xpastor/skima:

Analysis of differentially methylated positions (DMPs) and detection of differentially methylated regions (DMRs).

1 2	differentialMethylation(M, targets, array.annot.gr, betas = ilogit2(M), interest.vars = NULL, outdir = getwd(), ncores = 1, invisible = T)

`M`	matrix with M values
`targets`	data frame with sample annotation to be used to run limma
`array.annot.gr`	GRanges object with array annotation
`betas`	matrix with Beta values
`interest.vars`	character vector with variables of interest, excluding the confounding factors
`outdir`	path to save results
`ncores`	integer. Number of cores to use to parallellize the DMR analysis
`invisible`	a boolean to determine if the output of 'missMethyl::gometh' is returned