R Observatory: Metrics for BEDMatrix version 2.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BEDMatrix

2.0.4

Extract Genotypes from a PLINK .bed File

11packages depend

20.8Kdownloads / year

72.2%test coverage

13/13checks pass

Overview

About

Maintained by Alexander GruenebergFirst published 2015-11-0613 releasesCRAN page ↗GitHub ↗

A matrix-like data structure that allows for efficient, convenient, and scalable subsetting of binary genotype/phenotype files generated by PLINK (https://www.cog-genomics.org/plink2), the whole genome association analysis toolset, without loading the entire file into memory.

Install

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

install.packages("BEDMatrix", 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("QuantGen/BEDMatrix")

Development version from QuantGen/BEDMatrix. 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-bedmatrix

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-BEDMatrix

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-BEDMatrix

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

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

72.2%

Coverage · measured lines

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 228 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

20.8K

CRAN downloads in the past year

Rank #3,335 · ~57/day · ~1.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

86130 days

3.2K90 days

20.8K1 year

Compare downloads with other packages →

Also on475 r2u35 autocran3.7K conda_forge

Repository

GitHub ↗ quantgen/bedmatrix

19Stars

2Forks

1Open issues

0Open PRs

0Releases

434Commits

1Contributors

rr-pkgcrangeneticsgenomicsplinkplink2bed

434 commits · Last activity 2024-09-06

Stars over time

2025-05-29 · 192026-07-07 · 19

Repository practices

Upstream repositoryBeta

Checks run against github.com/quantgen/bedmatrix on 2026-08-23.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (2)

methodscrochet

LinkingTo (0)

none

Suggests (3)

data.table LinkedMatrix tinytest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

11direct

1indirect

BGData CoxMK hirisplexr jackstraw mrMLM phers genio groupedSurv popkin simtrait symDMatrix

Code & Tests

People & History

People (2)

Maintainer (1)

Alexander Grueneberg

Author, Maintainer

Authors (1)

Alexander Grueneberg

Author, Maintainer

Contributors (1)

Gustavo de los Campos

Contributor

Listed in earlier versions (1)

Lian Lian

no longer listed · 1.0.0 to 1.5.0

Package Timeline

13 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
2.0.4Latest
2024-09-06 · current release · diff ↗
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
2.0.3
2020-07-08 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.0.2
2020-03-11 · diff ↗
2.0.1
2019-12-16 · diff ↗
1.6.1
2019-06-21 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.5.0
2019-04-25 · diff ↗
1.4.1
2018-08-06 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 9 earlier events

1.4.0
2017-05-07 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.3.0
2016-09-28 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.2.0
2016-03-05 · diff ↗
1.1.0
2015-11-30 · diff ↗
1.0.1
2015-11-12 · diff ↗
1.0.0
2015-11-06
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-11-06
Total releases: 13 / 11 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Download size: 51 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BEDMatrix")

Format

Grueneberg, A., & de los Campos, G. (2024). BEDMatrix: Extract Genotypes from a PLINK .bed File (Version 2.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.BEDMatrix

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 BEDMatrix version 2.0.4 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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