A Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see Manipur et al (2024, Nature Communications) <doi:10.1038/s41467-024-49990-8>.
| Version: | 1.4.2 |
| Depends: | R (≥ 3.5.0) |
| Imports: | Rcpp (≥ 1.0.7), coloc, data.table, ggplot2, ggrepel, pheatmap, methods, viridis, stats, grDevices, magrittr, utils, matrixStats, dplyr |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | knitr, testthat (≥ 3.0.0), rmarkdown, RColorBrewer, ggpubr |
| Published: | 2025-07-30 |
| DOI: | 10.32614/CRAN.package.cophescan |
| Author: | Ichcha Manipur [aut, cre], Chris Wallace [aut] |
| Maintainer: | Ichcha Manipur <im504 at cam.ac.uk> |
| BugReports: | https://github.com/ichcha-m/cophescan/issues |
| License: | GPL-3 |
| URL: | https://github.com/ichcha-m/cophescan, https://ichcha-m.github.io/cophescan/ |
| NeedsCompilation: | yes |
| Citation: | cophescan citation info |
| Materials: | README, NEWS |
| CRAN checks: | cophescan results |
| Reference manual: | cophescan.html , cophescan.pdf |
| Vignettes: |
CoPheScan: Example with Fixed Priors (source, R code) CoPheScan: Example with Hierarchical Priors (source, R code) CoPheScan: Input data (source, R code) Introduction to CoPheScan (source, R code) |
| Package source: | cophescan_1.4.2.tar.gz |
| Windows binaries: | r-devel: cophescan_1.4.2.zip, r-release: cophescan_1.4.2.zip, r-oldrel: cophescan_1.4.2.zip |
| macOS binaries: | r-release (arm64): cophescan_1.4.2.tgz, r-oldrel (arm64): cophescan_1.4.2.tgz, r-release (x86_64): cophescan_1.4.2.tgz, r-oldrel (x86_64): cophescan_1.4.2.tgz |
| Old sources: | cophescan archive |
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