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.
Package details |
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Maintainer | Hannah Meyer <hannah.v.meyer@gmail.com> |
License | MIT + file LICENSE |
Version | 0.3.4 |
URL | https://meyer-lab-cshl.github.io/plinkQC/ |
Package repository | View on GitHub |
Installation |
Install the latest version of this package by entering the following in R:
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