plinkQC: Genotype Quality Control with 'PLINK'

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.

Version:	0.3.4
Depends:	R (≥ 3.6.0)
Imports:	methods, optparse, data.table (≥ 1.11.0), R.utils, ggplot2, ggforce, ggrepel, cowplot, UpSetR, dplyr, igraph (≥ 1.2.4), sys
Suggests:	testthat, mockery, formatR, knitr, rmarkdown
Published:	2021-07-15
DOI:	10.32614/CRAN.package.plinkQC
Author:	Hannah Meyer [aut, cre]
Maintainer:	Hannah Meyer <hannah.v.meyer at gmail.com>
BugReports:	https://github.com/meyer-lab-cshl/plinkQC/issues
License:	MIT + file LICENSE
URL:	https://meyer-lab-cshl.github.io/plinkQC/
NeedsCompilation:	no
SystemRequirements:	plink (1.9)
Materials:	README, NEWS
CRAN checks:	plinkQC results

Documentation:

Reference manual:	plinkQC.html , plinkQC.pdf
Vignettes:	AncestryCheck (source, R code) 1000Genomes (source, R code) HapMap (source, R code) GenotypeQC_with_plinkQC (source, R code)

Downloads:

Package source:	plinkQC_0.3.4.tar.gz
Windows binaries:	r-devel: plinkQC_0.3.4.zip, r-release: plinkQC_0.3.4.zip, r-oldrel: plinkQC_0.3.4.zip
macOS binaries:	r-release (arm64): plinkQC_0.3.4.tgz, r-oldrel (arm64): plinkQC_0.3.4.tgz, r-release (x86_64): plinkQC_0.3.4.tgz, r-oldrel (x86_64): plinkQC_0.3.4.tgz
Old sources:	plinkQC archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=plinkQC to link to this page.