M3D_Wrapper: Computes the components of the M3D test-statistic over all...
In M3D: Identifies differentially methylated regions across testing groups

Description Usage Arguments Value Author(s) References Examples

Returns the two components of the M3D test-statistic - the MMD (Gretton et al. 2006) for the full data and the coverge only data, respectively - for all regions and all samples pairs, as a matrix.

1	M3D_Wrapper(rrbs, overlaps, para = FALSE)

`rrbs`	An rrbs object containing methylation and coverage data as created using the BiSeq pacakge
`overlaps`	The overlaps between the list of testing regions and the methylation data. This is obtained using the function findOverlaps(CpGs,rrbs) for a GRanges object CpGs detailing the testing regions.
`para`	Set to true if called via M3D_Para

This returns the two components of the M3D test-statistic for each region over all sample pairs as a matrix. Subtracting them gives the M3D test-statistic. This is processed with the function pvals.

Tom Mayo t.mayo@ed.ac.uk

Gretton, A., Borgwardt, K. M., Rasch, M., Scholkopf, B., Smola, A. J. (2006). A kernel method for the two-sample-problem. In Advances in neural information processing systems (pp. 513-520).

data(rrbsDemo)
data(CpGsDemo)
CpGsDemo <- CpGsDemo[1:5]
overlaps <- GenomicRanges::findOverlaps(CpGsDemo,rrbsDemo)
M3D_list <- M3D_Wrapper(rrbsDemo,overlaps)
head(M3D_list$Full-M3D_list$Coverage)