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

Zongli Xu; Changchun Xie; Jack A Taylor; Liang Niu

doi:10.1093/bioinformatics/btaa732

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

Bioinformatics. 2021 May 5;37(5):711-713. doi: 10.1093/bioinformatics/btaa732.

Authors

Zongli Xu¹, Changchun Xie², Jack A Taylor^{1

3}, Liang Niu²

Affiliations

¹ Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
² Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
³ Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.

Abstract

Summary: 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.

Availability and implementation: ipDMR is available at https://bioconductor.org/packages/release/bioc/html/ENmix.html.

Supplementary information: Supplementary data are available at Bioinformatics online.

Published by Oxford University Press 2020.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural

MeSH terms

Epigenome*
Software*

Abstract

Publication types

MeSH terms

Grants and funding