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: 0.2.0
Depends: R (≥ 3.3.0)
Imports: methods, optparse, data.table (≥ 1.11.0), R.utils, ggplot2, ggforce, ggrepel, cowplot, UpSetR, dplyr, sys
Suggests: testthat, knitr, rmarkdown
Published: 2018-11-09
Author: Hannah Meyer ORCID iD [aut, cre]
Maintainer: Hannah Meyer <hannah at ebi.ac.uk>
BugReports: https://github.com/HannahVMeyer/plinkQC/issues
License: MIT + file LICENSE
URL: https://github.com/HannahVMeyer/plinkQC
NeedsCompilation: no
SystemRequirements: plink (1.9)
Materials: README NEWS
CRAN checks: plinkQC results

Downloads:

Reference manual: plinkQC.pdf
Vignettes: AncestryCheck
1000Genomes
HapMap
GenotypeQC_with_plinkQC
Package source: plinkQC_0.2.0.tar.gz
Windows binaries: r-devel: plinkQC_0.2.0.zip, r-release: plinkQC_0.2.0.zip, r-oldrel: plinkQC_0.2.0.zip
OS X binaries: r-release: plinkQC_0.2.0.tgz, r-oldrel: plinkQC_0.2.0.tgz
Old sources: plinkQC archive

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