R Observatory: Metrics for COMBAT version 0.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

COMBAT

0.0.4Package record

A Combined Association Test for Genes using Summary Statistics

0packages depend

2.9Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Minghui WangCRAN page ↗

Genome-wide association studies (GWAS) have been widely used for identifying common variants associated with complex diseases. Due to the small effect sizes of common variants, the power to detect individual risk variants is generally low. Complementary to SNP-level analysis, a variety of gene-based association tests have been proposed. However, the power of existing gene-based tests is often dependent on the underlying genetic models, and it is not known a priori which test is optimal. Here we proposed COMBined Association Test (COMBAT) to incorporate strengths from multiple existing gene-based tests, including VEGAS, GATES and simpleM. Compared to individual tests, COMBAT shows higher overall performance and robustness across a wide range of genetic models. The algorithm behind this method is described in Wang et al (2017) doi:10.1534/genetics.117.300257.

Install

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

install.packages("COMBAT", 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-combat

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-COMBAT

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-COMBAT

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Minghui Wang <m.h.wang@live.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Minghui",
                      family = "Wang",
                      role = c("aut", "cre"),
                      email = "m.h.wang@live.com"),
               person(given = "Yiyuan",
                      family = "Liu",
                      role = "aut"),
               person(given = "Shizhong",
                      family = "Han",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 54 s · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.4

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 67%2 run in a plain check · 1 hold no code
Exported functions with examples: 75%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 25%

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #13,872 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

26230 days

85590 days

2.9K1 year

Compare downloads with other packages →

Also on92 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing COMBAT adds 2 packages (1 with compiled code, 1.0 MB of source tarballs). Heaviest: mvtnorm 1.0 MB, corpcor 22 KB.

Depends (3)

R >= 3.2.0mvtnorm corpcor

Imports (0)

none

LinkingTo (0)

none

Suggests (1)

parallel

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (3)

Minghui Wang

Yiyuan Liu

· added in 0.0.4

Shizhong Han

Maintainer since 0.0.2 (2017)

Listed in earlier versions (2)

Jianfei Huang

no longer listed · 0.0.2

James B. Potash

no longer listed · 0.0.2

Releases (2)

Pick two releases to compare their code metrics.

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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.0.4Latest
record
2018-01-14 · current release · diff ↗ ·
added 2 exports
simpleM, ld.Rsquare
R
R 3.4.0 released · 2017-04-21
0.0.2
record
2017-01-11
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-01-11
Total releases: 2 / 9 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.2.0
Download size: 6.4 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("COMBAT")

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 COMBAT version 0.0.4 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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