R Observatory: Metrics for BEDMatrix version 2.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BEDMatrix

2.0.4Package record

Extract Genotypes from a PLINK .bed File

6packages dependsuggested by 5

16.8Kdownloads / year

72.2%test coverage

13/13flavors OK

Overview

About

Maintained by Alexander GruenebergCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 2.0.4

Use prefixed Calloc and Free to comply with CRAN.

From NEWS.md in the release

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. 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-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). 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

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.4

READMEYes · 228 wordsVignettesNoNEWSYes · 100% structured · mentions 2.0.4Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 3includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

16.8K

CRAN downloads in the past year

Rank #3,412 · ~46/day · ~1.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

3.2K90 days

16.8K1 year

Compare downloads with other packages →

Also on569 r2u23 autocran4.4K conda_forge

How downloads are counted

Repository

quantgen/bedmatrix ↗Organization: QuantGen

18Stars

2Forks

1Open issues

0Open PRs

0Releases

434Commits

1Commit identities

rr-pkgcrangeneticsgenomicsplinkplink2bed

434 commits · Last activity 2024-09-06 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 23
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-05-29 · 192026-09-11 · 18

How these are measured

PracticesBeta

Checks run against github.com/quantgen/bedmatrix on 2026-10-18.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing BEDMatrix adds 1 package (0 with compiled code, 28 KB of source tarballs). Heaviest: crochet 28 KB.

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

6direct

1indirect

Depends 1 · Imports 5

Suggested by 5

Depends, Imports or LinkingTo, most downloaded first

jackstraw BGData mrMLM phers CoxMK hirisplexr

Suggests, most downloaded first

genio popkin groupedSurv symDMatrix simtrait

How these are counted

Code & Tests

People & History

People (2)

Alexander Grueneberg

Author, Maintainer since 1.0.0 (2015)

Gustavo de los Campos

Contributor

Listed in earlier versions (1)

Lian Lian

no longer listed · 1.0.0 to 1.5.0

Releases (13)

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

Show 9 earlier eventsHide 9 earlier events

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

Cite

Cite this package

Run in R for the authors' entry:

citation("BEDMatrix")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1534/g3.119.400018.

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 v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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