Package: plinkQC
Type: Package
Title: Genotype Quality Control with 'PLINK'
Version: 1.1.0
Authors@R: c(
    person("Hannah", "Meyer", email = "hannah.v.meyer@gmail.com",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4564-0899")),
    person("Caroline", "Walter", email= "carowalter26@hotmail.com",
    role = c("ctb")),
    person("Maha", "Syed", email= "maha.s.syed@gmail.com",
    role = c("ctb")))
URL: https://meyer-lab-cshl.github.io/plinkQC/
BugReports: https://github.com/meyer-lab-cshl/plinkQC/issues
Maintainer: Hannah Meyer <hannah.v.meyer@gmail.com>
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)
        <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.
Depends: R (>= 3.6.0)
Imports: methods, optparse, data.table (>= 1.11.0), R.utils, ggplot2,
        ggrepel, cowplot, UpSetR, dplyr, igraph (>= 1.2.4), sys,
        randomForest, stats, tidyr
Suggests: testthat, mockery, formatR, knitr, rmarkdown
License: MIT + file LICENSE
SystemRequirements: plink (1.9)
Encoding: UTF-8
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev
Repository: https://meyer-lab-cshl.r-universe.dev
Date/Publication: 2026-03-27 16:10:50 UTC
RemoteUrl: https://github.com/meyer-lab-cshl/plinkqc
RemoteRef: HEAD
RemoteSha: 800cce05349d211e67203e89f511c72df3a760fb
NeedsCompilation: no
Packaged: 2026-07-03 19:11:03 UTC; root
Author: Hannah Meyer [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4564-0899>),
  Caroline Walter [ctb],
  Maha Syed [ctb]