SEAGLE

1.0.1

Scalable Exact Algorithm for Large-Scale Set-Based Gene-Environment Interaction Tests

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Jocelyn ChiFirst published 2021-06-072 releasesCRAN page ↗GitHub ↗

The explosion of biobank data offers immediate opportunities for gene-environment (GxE) interaction studies of complex diseases because of the large sample sizes and rich collection in genetic and non-genetic information. However, the extremely large sample size also introduces new computational challenges in GxE assessment, especially for set-based GxE variance component (VC) tests, a widely used strategy to boost overall GxE signals and to evaluate the joint GxE effect of multiple variants from a biologically meaningful unit (e.g., gene). We present 'SEAGLE', a Scalable Exact AlGorithm for Large-scale Set-based GxE tests, to permit GxE VC test scalable to biobank data. 'SEAGLE' employs modern matrix computations to achieve the same “exact” results as the original GxE VC tests, and does not impose additional assumptions nor relies on approximations. 'SEAGLE' can easily accommodate sample sizes in the order of 10^5, is implementable on standard laptops, and does not require specialized equipment. The accompanying manuscript for this package can be found at Chi, Ipsen, Hsiao, Lin, Wang, Lee, Lu, and Tzeng. (2021+) arXiv:2105.03228.

Install

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

install.packages("SEAGLE", 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("jocelynchi/SEAGLE")

Development version from jocelynchi/SEAGLE. 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-seagle

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

# 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-SEAGLE

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: 7.9 min · r-release-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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

Documentation

READMEYes · 317 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #18,891 · ~7/day · ~202/mo

Releases R versions

Daily download trend is not available in this view yet.

18330 days

59990 days

2.4K1 year

Compare downloads with other packages →

Also on91 r2u31 autocran

Repository

GitHub ↗ jocelynchi/seagle

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2021-11-05

Repository practices

Upstream repositoryBeta

Checks run against github.com/jocelynchi/seagle on 2026-07-26.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.5.0MatrixCompQuadForm

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

rmarkdown knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Jocelyn Chi

Author, Maintainer

Authors (3)

Jocelyn Chi

Author, Maintainer

Ilse Ipsen

Author

Jung-Ying Tzeng

Author

Package 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
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
R
R 4.2.0 released · 2022-04-22
1.0.1Latest
2021-11-05 · current release · diff ↗
1.0.0
2021-06-07
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-06-07
Total releases: 2 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 59 KB / 1 file
Download size: 326 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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