M3D_Single: Computes the components of the M3D test-statistic over one...
In M3D: Identifies differentially methylated regions across testing groups

Description Usage Arguments Value Author(s) References

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. This is not intended to be called directly by the user.

1	M3D_Single(test_data, loc_mx, locInds, method = "MinusCovMMD")

`test_data`	Contains the methylation data over two samples for a given region.
`loc_mx`	The matrix of distances between the CpG sites.
`locInds`	The indices of the non-zero entries of loc_mx.
`method`	This specifies whether to return the full MMD and the methylation blind MMD (focusing only on the coverage) or just the former. if method ='MinusCovMMD' it is both, all other values return just the full MMD.

This returns the value of the MMD for the region between the two samples as a numeric. If method is set to 'MinusCovMMD', a list is returned of the full MMD and the coverage only MMD. Subtracting them gives the M3D test-statistic.

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).

M3D documentation built on April 29, 2020, 5:59 a.m.