PathwayVote: Robust Pathway Enrichment for DNA Methylation Studies Using Ensemble Voting

Performs pathway enrichment analysis using a voting-based framework that integrates CpG–gene regulatory information from expression quantitative trait methylation (eQTM) data. For a grid of top-ranked CpGs and filtering thresholds, gene sets are generated and refined using an entropy-based pruning strategy that balances information richness, stability, and probe bias correction. In particular, gene lists dominated by genes with disproportionately high numbers of CpG mappings are penalized to mitigate active probe bias—a common artifact in methylation data analysis. Enrichment results across parameter combinations are then aggregated using a voting scheme, prioritizing pathways that are consistently recovered under diverse settings and robust to parameter perturbations.

Version: 0.1.1
Depends: R (≥ 4.0.0)
Imports: AnnotationDbi, clusterProfiler, future, furrr, GO.db, methods, org.Hs.eg.db, parallelly, reactome.db
Suggests: testthat
Published: 2025-06-25
DOI: 10.32614/CRAN.package.PathwayVote
Author: Yinan Zheng ORCID iD [aut, cre]
Maintainer: Yinan Zheng <y-zheng at northwestern.edu>
License: MIT + file LICENSE
NeedsCompilation: no
CRAN checks: PathwayVote results

Documentation:

Reference manual: PathwayVote.pdf

Downloads:

Package source: PathwayVote_0.1.1.tar.gz
Windows binaries: r-devel: PathwayVote_0.1.1.zip, r-release: PathwayVote_0.1.1.zip, r-oldrel: PathwayVote_0.1.1.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): PathwayVote_0.1.1.tgz, r-oldrel (x86_64): PathwayVote_0.1.1.tgz
Old sources: PathwayVote archive

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