dnachun / packages / r-plinkqc

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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.

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