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 |
| 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.pdf |
| Vignettes: |
AncestryCheck 1000Genomes HapMap GenotypeQC_with_plinkQC |
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.