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PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework.

Yinan Zheng·Feng Gao·Lifang Hou
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Abstract

MOTIVATION: Pathway enrichment analysis is commonly used to interpret epigenomewide association studies, yet conventional methods often rely on arbitrary thresholds and simplified CpG-gene mappings, making them sensitive to analytical choices and unable to fully leverage CpG-gene relationships Recent advances in expression quantitative trait methylation (eQTM) studies offer a rich resource to refine these mappings, but are rarely utilized in DNA methylation enrichment pipelines. RESULTS: We developed PathwayVote, an R package that implements a voting-based consensus approach and leverages eQTM data to identify robustly enriched pathways. PathwayVote reduces dependence on arbitrary cutoffs and improves sensitivity and reproducibility of enrichment results. AVAILABILITY AND IMPLEMENTATION: PathwayVote is freely available on GitHub (https://github.com/YinanZheng/PathwayVote) under the GPL-3 license and CRAN: https://CRAN.R-project.org/package=PathwayVote. The version of the code corresponding to this manuscript has been archived on Zenodo (https://doi.org/10.5281/zenodo.17209507).

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HumansCpG IslandsDNA MethylationEpigenomicsQuantitative Trait LociSoftwareVotingConsensusJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, N.I.H., Extramural

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Yinan Zheng, Feng Gao, Lifang Hou. 2025-11-01. PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework.. https://doi.org/10.1093/bioinformatics%2Fbtaf590

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