PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework.
Where this comes from
- Record sourced from PubMed, PMID 41143682.
- Also identified by DOI 10.1093/bioinformatics/btaf590 and PMC identifier 12596613.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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. 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 The version of the code corresponding to this manuscript has been archived on Zenodo (https://doi.org/10.5281/zenodo.17209507).
Medical subject headings
- DNA Methylation
- Epigenomics
- Software