R Observatory: Metrics for ofGEM version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ofGEM

1.0

A Meta-Analysis Approach with Filtering for Identifying Gene-Level Gene-Environment Interactions with Genetic Association Data

0packages depend

2.2Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Jiebiao WangFirst published 2018-07-131 releasesCRAN page ↗GitHub ↗

Offers a gene-based meta-analysis test with filtering to detect gene-environment interactions (GxE) with association data, proposed by Wang et al. (2018) doi:10.1002/gepi.22115. It first conducts a meta-filtering test to filter out unpromising SNPs by combining all samples in the consortia data. It then runs a test of omnibus-filtering-based GxE meta-analysis (ofGEM) that combines the strengths of the fixed- and random-effects meta-analysis with meta-filtering. It can also analyze data from multiple ethnic groups.

Install

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

install.packages("ofGEM", repos = "https://cloud.r-project.org/")

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("randel/ofGEM")

Development version from randel/ofGEM. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ofgem

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ofGEM

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

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-ofGEM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 53 s · r-release-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 33%

Downloads

2.2K

CRAN downloads in the past year

Rank #18,750 · ~6/day · ~183/mo

Releases R versions

Daily download trend is not available in this view yet.

14830 days

58490 days

2.2K1 year

Compare downloads with other packages →

Also on118 r2u9 autocran80 c2d4u

Repository

GitHub ↗ randel/ofgem

3Stars

0Forks

0Open issues

0Open PRs

0Releases

6Commits

1Contributors

6 commits · Last activity 2018-07-07

Stars over time

2022-10-27 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/randel/ofgem on 2026-08-16.

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (3)

CompQuadFormMASSforestplot

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (3)

Lin S. Chen

no longer listed · 1.0

Qianying Liu

no longer listed · 1.0

Jiebiao Wang

no longer listed · 1.0

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2018-07-13
Total releases: 1 / 8 yrs
License: GPL
Bundled data: 5.1 KB / 1 file
Download size: 11 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Meta-Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ofGEM")

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ofGEM version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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