PathwayVote
Robust Pathway Enrichment for DNA Methylation Studies Using Ensemble Voting
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.
Downloads
197
Last 30 days
22593rd
649
Last 90 days
2.1K
Last year
Trend: +8.2% (30d vs prior 30d)
CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (2 non-OK)
package dependencies
Packages suggested but not available for checking: 'GO.db', 'reactome.db'
whether package can be installed
Installation failed. See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/PathwayVote.Rcheck/00install.out’ for details.
Check History
ERROR 12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Package required but not available: ‘clusterProfiler’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages suggested but not available for checking: 'GO.db', 'reactome.db'