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plinkQC
View on CRAN: Click
here
Download and install plinkQC package within the R console
Install from CRAN:
install.packages("plinkQC")
Install from Github:
library("remotes")
install_github("cran/plinkQC") Install by package version:
library("remotes")
install_version("plinkQC", "1.0.0") Attach the package and use:
library("plinkQC")
Maintained by
Hannah Meyer
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-11-04
Latest Update: 2021-07-15
Description:
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) . 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.
How to cite:
Hannah Meyer (2018). plinkQC: Genotype Quality Control with 'PLINK'. R package version 1.0.0, https://cran.r-project.org/web/packages/plinkQC. Accessed 04 Jun. 2026.
Previous versions and publish date:
0.1.0 (2018-11-04 17:00), 0.1.1 (2018-11-06 13:20), 0.2.0 (2018-11-09 15:20), 0.2.1 (2019-03-01 22:50), 0.2.2 (2019-06-19 23:40), 0.2.3 (2019-09-25 17:00), 0.3.0 (2019-10-19 07:20), 0.3.2 (2020-07-07 16:00), 0.3.3 (2021-02-08 23:40), 0.3.4 (2021-07-15 17:40), 1.0.0 (2025-11-25 22:10), 1.0.1 (2026-02-09 23:00)
Other packages that cited plinkQC R package
View plinkQC citation profile
Other R packages that plinkQC depends,
imports, suggests or enhances
Complete documentation for plinkQC
Functions, R codes and Examples using
the plinkQC R package
Some associated functions: checkFiltering . checkPlink . checkRemoveIDs . check_ancestry . check_het_and_miss . check_hwe . check_maf . check_relatedness . check_sex . check_snp_missingness . cleanData . evaluate_check_ancestry . evaluate_check_het_and_miss . evaluate_check_relatedness . evaluate_check_sex . overviewPerIndividualQC . overviewPerMarkerQC . perIndividualQC . perMarkerQC . plinkQC . relatednessFilter . run_check_ancestry . run_check_heterozygosity . run_check_missingness . run_check_relatedness . run_check_sex . testNumerics .
Some associated R codes: applyQC.R . individualQC.R . markerQC.R . plinkQC.R . utils.R . Full plinkQC package functions and examples
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