ipDMR: identification of differentially methylated regions with interval P-values | Zendy

Zongli Xu | Zendy; Changchun Xie | Zendy; Jack A. Taylor | Zendy; Liang Niu | Zendy

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ipDMR: identification of differentially methylated regions with interval P-values

Author(s) -

Zongli Xu,

Changchun Xie,

Jack A. Taylor,

Liang Niu

Publication year - 2020

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa732

Subject(s) - identification (biology) , interval (graph theory) , computational biology , biology , genetics , mathematics , combinatorics , ecology

ipDMR is an R software tool for identification of differentially methylated regions (DMRs) using auto-correlated P-values for individual CpGs from epigenome-wide association analysis using array or bisulfite sequencing data. It summarizes P-values for adjacent CpGs, identifies association peaks and then extends peaks to find boundaries of DMRs. ipDMR uses BED format files as input and is easy to use. Simulations guided by real data found that ipDMR outperformed current available methods and provided slightly higher true positive rates and much lower false discovery rates.

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