GBJ

0.5.4

Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies

1packages depend

5Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Ryan SunFirst published 2017-08-305 releasesCRAN page ↗

Offers the Generalized Berk-Jones (GBJ) test for set-based inference in genetic association studies. The GBJ is designed as an alternative to tests such as Berk-Jones (BJ), Higher Criticism (HC), Generalized Higher Criticism (GHC), Minimum p-value (minP), and Sequence Kernel Association Test (SKAT). All of these other methods (except for SKAT) are also implemented in this package, and we additionally provide an omnibus test (OMNI) which integrates information from each of the tests. The GBJ has been shown to outperform other tests in genetic association studies when signals are correlated and moderately sparse. Please see the vignette for a quickstart guide or Sun and Lin (2017) arXiv:1710.02469 for more details.

Install

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

install.packages("GBJ", 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-gbj

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-GBJ

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-GBJ

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: 3.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.41

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 280 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

CRAN downloads in the past year

Rank #12,747 · ~14/day · ~419/mo

Releases R versions

Daily download trend is not available in this view yet.

25630 days

84190 days

5K1 year

Compare downloads with other packages →

Also on484 r2u22 autocran6.3K conda_forge

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (5)

Rcpp mvtnorm SKATstatsBH

LinkingTo (2)

Rcpp BH

Suggests (5)

knitr rmarkdown bindata rje testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

sGBJ

Code & Tests

Code Composition

R 2,077 (60%)Rd 648 (19%)C++ 619 (18%)Vignettes 129 (4%)

Code characteristics

Cyclomatic complexity: 4.5 median / 14 max
Test cases: 9 / 0.41 per code line

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

34 19 exported

Complexity

5.5 avg / 14 max

Call network

34 nodes / 41 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Datasets

Bundled datasets · 1

Name	Class	Rows × Cols	Also ships in
FGFR2	data.frame	91 × 64	–

People & History

People (1)

Maintainer (1)

Ryan Sun

Author, Maintainer

Authors (1)

Ryan Sun

Author, Maintainer

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
0.5.4Latest
2024-01-31 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.5.3
2020-01-13 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.5.2
2018-06-27 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.5.0
2017-10-06 · diff ↗
0.4.0
2017-08-30
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-08-30
Total releases: 5 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 4.2 KB / 2 files
Download size: 49 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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