CRAN/E | plinkQC

plinkQC

Genotype Quality Control with 'PLINK'

Installation

About

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.

meyer-lab-cshl.github.io/plinkQC/
System requirements plink (1.9)
Bug report File report

Key Metrics

Version 0.3.4
R ≥ 3.6.0
Published 2021-07-15 1176 days ago
Needs compilation? no
License MIT
License File
CRAN checks plinkQC results

Downloads

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Maintainer

Maintainer

Hannah Meyer

Authors

Hannah Meyer

aut / cre

Material

README
NEWS
Reference manual
Package source

Vignettes

AncestryCheck
1000Genomes
HapMap
GenotypeQC_with_plinkQC

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

plinkQC archive

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

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