M3D_Single: Computes the components of the M3D test-statistic over one...

In TomMayo/M3Ddevel: (development for M3D) Identifies differentially methylated regions across testing groups

Description

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.

Usage

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

Arguments

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.

Value

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.

Author(s)

Tom Mayo [e-mail]

References

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).

TomMayo/M3Ddevel documentation built on May 9, 2019, 4:53 p.m.