cophescan

1.4.3

Adaptation of the Coloc Method for PheWAS

0packages depend

5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Ichcha ManipurFirst published 2023-10-255 releasesCRAN page ↗GitHub ↗

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>.

Install

R (CRAN)pak (dev)Ubuntu (r2u)openSUSE (OBS)

install.packages("cophescan")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

pak::pak("ichcha-m/cophescan")

Development version from ichcha-m/cophescan. Requires the pak package.

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-cophescan

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

bspm (used by r2u) also needs make: sudo apt install make

sudo zypper install R-cophescan

RPMs auto-built from CRAN on openSUSE OBS.

Health

CRAN checks

13OK

Code health

Yes

Tests · ratio 0.09

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

CRAN downloads in the past year

Rank #6,279 · ~14/day · ~415/mo

Releases R versions

cophescan

Daily download trend is not available in this view yet.

Compare downloads with other packages →

58930 days

1.7K90 days

5K1 year

Also on495 r2u27 autocran

Source & community

GitHub ↗

Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (14)

Rcpp coloc data.table ggplot2 ggrepel pheatmap methods baseviridis stats basegrDevices basemagrittr utils basematrixStats dplyr

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (5)

knitr testthat rmarkdown RColorBrewer ggpubr

Enhances (0)

none

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,924 (41%)Rd 1,477 (31%)C++ 792 (17%)Vignettes 541 (11%)

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

90 15 exported

Complexity

2.8 avg / 19 max

Call network

90 nodes / 70 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Ichcha Manipur

Author, Maintainer

Authors (1)

Chris Wallace

Author

Release timeline

5 releases. Pick two to compare their code metrics; R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.4.3Latest
2026-03-18 · current release
1.4.2
2025-07-30 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.4.1
2024-06-11 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.4.0
2024-03-11 · diff ↗
1.3.2
2023-10-25

Package metadata

First published: 2023-10-25
Total releases: 5 / 3 yrs
License: GPL-3 OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet