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MethCP: Differentially Methylated Region Detection with Change Point Models

By Boying Gong, Elizabeth F Purdom

Posted 13 Feb 2018
bioRxiv DOI: 10.1101/265116 (published DOI: 10.1089/cmb.2019.0326)

Whole-genome bisulfite sequencing (WGBS) provides a precise measure of methylation across the genome, yet pose a challenge on identifying regions that are differentially methylated (DMRs) between different conditions. A number of methods have been proposed, mainly by performing tests on individual methylation locus and combining significant positions. While this approach can globally control locus-level error rates, in the detection of a region, these methods often result in poor estimates. We develop a DMR detecting method MethCP for WGBS data based on change point detection, which naturally segments the genome and provide region-level differential analysis. We demonstrate the performance of MethCP on a senescent cell study, an Arabidopsis dataset and a simulated dataset. We compare our method to four developed methods and we show MethCP is more accurate in detecting the complete DM region.

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