M3D: a kernel-based test for spatially correlated changes in methylation profiles.
Bottom Line: DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance.The test statistic explicitly accounts for differences in coverage levels between samples, thus handling in a principled way a major confounder in the analysis of methylation data.Empirical tests on real and simulated datasets show an increased power compared to established methods, as well as considerable robustness with respect to coverage and replication levels.
Affiliation: IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.Show MeSH
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Mentions: The M3D statistic will therefore be different from zero when there is a change in the methylation profile, independently of a change in the coverage profile. As a consequence, M3D between replicate RRBS experiments (which do not necessarily have identical coverage) should be close to zero or, equivalently, the full MMD should be equal to the coverage MMD. This is borne out in the data; the metrics strongly agree over replicates. Testing equality of metrics over 102 ENCODE RRBS datasets gives an R2 of 0.95. This can be seen in Supplementary Figure 2; specific examples can also be seen in Figures 2(a–c) and 4(a–c), where the dense region around the diagonal represents unchanged DMRs with M3D close to zero.Fig. 2.
Affiliation: IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.