Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
Bioinformatics. 2021 May 5;37(5):711-713. doi: 10.1093/bioinformatics/btaa732.
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.
ipDMR is available at https://bioconductor.org/packages/release/bioc/html/ENmix.html.
Supplementary data are available at Bioinformatics online.
ipDMR 是一个 R 软件工具,用于识别差异甲基化区域(DMRs),方法是使用来自数组或亚硫酸氢盐测序数据的全基因组关联分析中单个 CpG 的自相关 P 值。它总结了相邻 CpG 的 P 值,识别关联峰,然后扩展峰以找到 DMRs 的边界。ipDMR 使用 BED 格式文件作为输入,使用方便。基于真实数据的模拟发现,ipDMR 优于当前可用的方法,并提供了略高的真阳性率和低得多的假发现率。
ipDMR 可在 https://bioconductor.org/packages/release/bioc/html/ENmix.html 获得。
补充数据可在生物信息学在线获得。