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 [email protected]

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).

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