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dmrff: identifying differentially methylated regions efficiently with power and control

By Matthew Suderman, James R. Staley, Robert French, Ryan Arathimos, Andrew J Simpkin, Kate Tilling

Posted 31 Dec 2018
bioRxiv DOI: 10.1101/508556

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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