CRAN/E | cophescan

cophescan

Adaptation of the Coloc Method for PheWAS

Installation

About

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.

Citation cophescan citation info
github.com/ichcha-m/cophescan
ichcha-m.github.io/cophescan/
Bug report File report

Key Metrics

Version 1.4.0
R ≥ 3.5.0
Published 2024-03-11 53 days ago
Needs compilation? yes
License GPL-3
CRAN checks cophescan results

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Maintainer

Maintainer

Ichcha Manipur

im504@cam.ac.uk

Authors

Ichcha Manipur

aut / cre

Chris Wallace

aut

Material

README
NEWS
Reference manual
Package source

Vignettes

CoPheScan: Example with Fixed Priors
CoPheScan: Example with Hierarchical Priors
CoPheScan: Input data
Introduction to CoPheScan

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

cophescan archive

Depends

R ≥ 3.5.0

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

LinkingTo

Rcpp
RcppArmadillo