cophescan: Adaptation of the Coloc Method for PheWAS

A Bayesian method for conducting Phenome-wide association studies (PheWAS) that simultaneously identifies causal associations between genetic variants and confounding due to linkage disequilibrium. For details see Manipur et al (2023) <doi:10.1101/2023.06.29.546856>.

Version: 1.3.2
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: 2023-10-25
Author: Ichcha Manipur [aut, cre], Chris Wallace [aut]
Maintainer: Ichcha Manipur <im504 at>
License: GPL-3
NeedsCompilation: yes
Citation: cophescan citation info
Materials: README NEWS
CRAN checks: cophescan results


Reference manual: cophescan.pdf
Vignettes: CoPheScan: Example with Fixed Priors
CoPheScan: Example with Hierarchical Priors
CoPheScan: Input data
Introduction to CoPheScan


Package source: cophescan_1.3.2.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): cophescan_1.3.2.tgz, r-oldrel (arm64): cophescan_1.3.2.tgz, r-release (x86_64): cophescan_1.3.2.tgz


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