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bioRxiv · 10.1101/508556

dmrff: identifying differentially methylated regions efficiently with power and control

Suderman, M.·Staley, J. R.·French, R.·Arathimos, R.·Simpkin, A.·Tilling, K.
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Abstract

A differentially methylated region (DMR) is a genomic region in which DNA methylation is consistently positively or negatively associated with a phenotype or exposure. We demonstrate that existing algorithms for identifying DMRs either fail to consistently control false positive rates (comb-p and DMRcate), suffer from low power (bumphunter) or lack modeling flexibility (seqlm). We introduce a new method, dmrff, that overcomes these shortcomings and can additionally be used to meta-analyze multiple datasets. When applied to investigate associations of age in multiple datasets, dmrff identifies novel DMRs near genes previously linked to age. An R implementation is available on Github (http://github.com/perishky/dmrff).

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Suderman, M., Staley, J. R., French, R., Arathimos, R., Simpkin, A., Tilling, K.. 2018-12-31. dmrff: identifying differentially methylated regions efficiently with power and control. https://doi.org/10.1101/508556

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