Package: plinkQC
Type: Package
Title: Genotype Quality Control with 'PLINK'
Version: 1.0.0
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: 7.3.2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-11-25 19:54:44 UTC; syed
Author: Hannah Meyer [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4564-0899>),
  Caroline Walter [ctb],
  Maha Syed [ctb]
Repository: CRAN
Date/Publication: 2025-11-25 21:10:02 UTC
Built: R 4.5.1; ; 2025-11-25 23:12:25 UTC; unix
