cophescan: Adaptation of the Coloc Method for PheWAS

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 (2023) <doi:10.1101/2023.06.29.546856>.

Version: 1.4.0
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: 2024-03-11
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

Documentation:

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

Downloads:

Package source: cophescan_1.4.0.tar.gz
Windows binaries: r-prerel: cophescan_1.4.0.zip, r-release: cophescan_1.4.0.zip, r-oldrel: cophescan_1.4.0.zip
macOS binaries: r-prerel (arm64): cophescan_1.4.0.tgz, r-release (arm64): cophescan_1.4.0.tgz, r-oldrel (arm64): cophescan_1.4.0.tgz, r-prerel (x86_64): cophescan_1.4.0.tgz, r-release (x86_64): cophescan_1.4.0.tgz
Old sources: cophescan archive

Linking:

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