GEInter

0.3.2

Robust Gene-Environment Interaction Analysis

0packages depend

2.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Xing QinFirst published 2021-01-215 releasesCRAN page ↗

Description: For the risk, progression, and response to treatment of many complex diseases, it has been increasingly recognized that gene-environment interactions play important roles beyond the main genetic and environmental effects. In practical interaction analyses, outliers in response variables and covariates are not uncommon. In addition, missingness in environmental factors is routinely encountered in epidemiological studies. The developed package consists of five robust approaches to address the outliers problems, among which two approaches can also accommodate missingness in environmental factors. Both continuous and right censored responses are considered. The proposed approaches are based on penalization and sparse boosting techniques for identifying important interactions, which are realized using efficient algorithms. Beyond the gene-environment analysis, the developed package can also be adopted to conduct analysis on interactions between other types of low-dimensional and high-dimensional data. (Mengyun Wu et al (2017), doi:10.1080/00949655.2018.1523411; Mengyun Wu et al (2017), doi:10.1002/gepi.22055; Yaqing Xu et al (2018), doi:10.1080/00949655.2018.1523411; Yaqing Xu et al (2019), doi:10.1016/j.ygeno.2018.07.006; Mengyun Wu et al (2021), doi:10.1093/bioinformatics/btab318).

Install

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

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

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

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-geinter

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-GEInter

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-GEInter

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

Health

CRAN checks

13OK

Slowest check: 4.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 87%

Downloads

2.8K

CRAN downloads in the past year

Rank #15,053 · ~8/day · ~237/mo

Releases R versions

Daily download trend is not available in this view yet.

24730 days

70790 days

2.8K1 year

Compare downloads with other packages →

Also on130 r2u

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

MASSsplinespcaPP Hmiscsurvivalquantreg reshape2 ggplot2statsgraphics

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Xing Qin

Author, Maintainer

Authors (3)

Xing Qin

Author, Maintainer

Shuangge Ma

Author

Mengyun Wu

Author

Package 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
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.3.2Latest
2022-05-19 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.1
2021-07-10 · diff ↗
unarchivedReturned to CRAN
2021-07-10
archivedRemoved from CRAN
2021-05-27
check problems were not corrected in time
R
R 4.1.0 released · 2021-05-18
0.3.0
2021-03-22 · diff ↗
0.2.0
2021-03-01 · diff ↗
0.1.0
2021-01-21
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-21
Total releases: 5 / 5 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.7 MB / 2 files
Download size: 2.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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