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