Package: cophescan
Title: Adaptation of the Coloc Method for PheWAS
Version: 1.4.3
Authors@R: c(person("Ichcha", "Manipur", role=c("aut","cre"),
    email = "im504@cam.ac.uk"),
    person("Chris", "Wallace", role=c("aut")))
Maintainer: Ichcha Manipur <im504@cam.ac.uk>
Description: 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>.
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 3.5.0)
URL: https://github.com/ichcha-m/cophescan,
        https://ichcha-m.github.io/cophescan/
BugReports: https://github.com/ichcha-m/cophescan/issues
Imports: Rcpp (>= 1.0.7), coloc, data.table, ggplot2, ggrepel,
        pheatmap, methods, viridis, stats, grDevices, magrittr, utils,
        matrixStats, dplyr
Suggests: knitr, testthat (>= 3.0.0), rmarkdown, RColorBrewer, ggpubr
Collate: 'cophescan-package.R' 'singlevar.R' 'multivarsusie.R'
        'multitrait.R' 'cophe_hyp_predict.R' 'copheplots.R'
        'testdata.R' 'RcppExports.R' 'metrop_hier_priors.R' 'zzz.R'
LinkingTo: Rcpp, RcppArmadillo
Config/testthat/edition: 3
ByteCompile: true
Repository: https://ichcha-m.r-universe.dev
Date/Publication: 2026-03-23 10:35:19 UTC
RemoteUrl: https://github.com/ichcha-m/cophescan
RemoteRef: HEAD
RemoteSha: c079a9f1caa87d98ac73d74e3d4c99910e93a78b
NeedsCompilation: yes
Packaged: 2026-06-21 08:42:27 UTC; root
Author: Ichcha Manipur [aut, cre],
  Chris Wallace [aut]