MPGE

1.0.1

A Two-Step Approach to Testing Overall Effect of Gene-Environment Interaction for Multiple Phenotypes

0packages depend

4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Arunabha MajumdarFirst published 2020-10-232 releasesCRAN page ↗GitHub ↗

Interaction between a genetic variant (e.g., a single nucleotide polymorphism) and an environmental variable (e.g., physical activity) can have a shared effect on multiple phenotypes (e.g., blood lipids). We implement a two-step method to test for an overall interaction effect on multiple phenotypes. In first step, the method tests for an overall marginal genetic association between the genetic variant and the multivariate phenotype. The genetic variants which show an evidence of marginal overall genetic effect in the first step are prioritized while testing for an overall gene-environment interaction effect in the second step. Methodology is available from: A Majumdar, KS Burch, T Haldar, S Sankararaman, B Pasaniuc, WJ Gauderman, JS Witte (2020) <doi:10.1093/bioinformatics/btaa1083>.

Install

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

install.packages("MPGE")

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

pak::pak("ArunabhaCodes/MPGE")

Development version from ArunabhaCodes/MPGE. 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-mpge

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 dnf copr enable iucar/cran

sudo dnf install R-CRAN-MPGE

RPMs from the iucar/cran COPR, rebuilt from CRAN.

sudo zypper install R-MPGE

RPMs auto-built from CRAN on openSUSE OBS.

Health

CRAN checks

13OK

Code health

Yes

Tests · ratio 0.32

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-19
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

CRAN downloads in the past year

Rank #7,257 · ~11/day · ~335/mo

49430 days

1.6K90 days

4K1 year

Also on107 r2u17 autocran

Source & community

GitHub ↗

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (4)

car purrr stats baseutils base

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown spelling testthat

Enhances (0)

none

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code

1,061Lines of code

3Exported functions

Code & tests

Open call graph →

Line coverage

–

Expression

–

Tests / Examples

–

Functions

7 3 exported

Complexity

8 avg / 26 max

Call network

7 nodes / 6 edges

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

Loading call graph…

Lowest coverage

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

People & History

People (2)

Maintainer (1)

Arunabha Majumdar

Author, Maintainer

Authors (1)

Tanushree Haldar

Author

Release timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
2026-03-12 · current release
1.0.0
2026-03-10

Package metadata

First published: 2020-10-23
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet