plinkQC

1.1.0

Genotype Quality Control with 'PLINK'

0packages depend

6.2Kdownloads / year

40.5%test coverage

13/13checks pass

Overview

About

Maintained by Hannah MeyerFirst published 2018-11-0413 releasesCRAN page ↗GitHub ↗

Genotyping arrays enable the direct measurement of an individuals genotype at thousands of markers. 'plinkQC' facilitates genotype quality control for genetic association studies as described by Anderson and colleagues (2010) doi:10.1038/nprot.2010.116. It makes 'PLINK' basic statistics (e.g. missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions accessible from 'R' and generates a per-individual and per-marker quality control report. Individuals and markers that fail the quality control can subsequently be removed to generate a new, clean dataset. Removal of individuals based on relationship status is optimised to retain as many individuals as possible in the study. Additionally, there is a trained classifier to predict genomic ancestry of human samples.

Install

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

install.packages("plinkQC", 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("meyer-lab-cshl/plinkQC")

Development version from meyer-lab-cshl/plinkQC. 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-plinkqc

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-plinkQC

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-plinkQC

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

Health

CRAN checks

13OK

Slowest check: 3.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 22.85

40.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: 100%
Return-value docs: 79%
References docs: 0%

Downloads

6.2K

CRAN downloads in the past year

Rank #5,167 · ~17/day · ~516/mo

Releases R versions

Daily download trend is not available in this view yet.

35230 days

1.7K90 days

6.2K1 year

Compare downloads with other packages →

Also on156 r2u1 autocran

Repository

GitHub ↗ meyer-lab-cshl/plinkqc

69Stars

26Forks

11Open issues

0Open PRs

9Releases

510Commits

11Contributors

510 commits · Last activity 2026-03-27

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/meyer-lab-cshl/plinkqc on 2026-07-30.

Continuous integration (1)

Travis CI

Docs source (1)

README.Rmd

Research and citation (1)

codemeta.json

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (14)

methodsoptparse data.table R.utils ggplot2 ggrepel cowplot UpSetR dplyr igraph sys randomForeststatstidyr

LinkingTo (0)

none

Suggests (5)

testthat mockery formatR knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Hannah Meyer

Author, Maintainer

Authors (1)

Hannah Meyer

Author, Maintainer

Contributors (2)

Maha Syed

Contributor · added in 1.0.0

Caroline Walter

Contributor · added in 1.0.0

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
1.1.0Latest
2026-03-27 · current release · diff ↗
1.0.1
2026-02-09 · diff ↗
1.0.0
2025-11-25 · diff ↗
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
0.3.4
2021-07-15 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.3
2021-02-08 · diff ↗
0.3.2
2020-07-07 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.3.0
2019-10-19 · diff ↗
0.2.3
2019-09-25 · diff ↗
0.2.2
2019-06-19 · diff ↗

Show 6 earlier events

R
R 3.6.0 released · 2019-04-26
0.2.1
2019-03-01 · diff ↗
0.2.0
2018-11-09 · diff ↗
0.1.1
2018-11-06 · diff ↗
0.1.0
2018-11-04
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-04
Total releases: 13 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Download size: 6.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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