Package: PathwayVote
Title: Robust Pathway Enrichment for DNA Methylation Studies Using
        Ensemble Voting
Version: 0.1.3
Authors@R: c(person("Yinan", "Zheng",
                    email = "y-zheng@northwestern.edu",
                    role = c("aut", "cre"),
                    comment = c(ORCID = "0000-0002-2006-7320")))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: harmonicmeanp, AnnotationDbi, clusterProfiler, future, furrr,
        methods, parallelly
Suggests: GO.db, org.Hs.eg.db, reactome.db, openxlsx
RoxygenNote: 7.3.2
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://yinanzheng.r-universe.dev
Date/Publication: 2026-01-19 16:33:30 UTC
RemoteUrl: https://github.com/yinanzheng/pathwayvote
RemoteRef: HEAD
RemoteSha: 4b84a436e33e8a72104d7b7a2f41525b470609bc
NeedsCompilation: no
Packaged: 2026-10-18 11:30:50 UTC; root
Author: Yinan Zheng [aut, cre] (ORCID: <https://orcid.org/0000-0002-2006-7320>)
Maintainer: Yinan Zheng <y-zheng@northwestern.edu>