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.

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Description file content

Package
plinkQC
Type
Package
Title
Genotype Quality Control with 'PLINK'
Version
0.2.1
URL
BugReports
https://github.com/HannahVMeyer/plinkQC/issues
Maintainer
Hannah Meyer
Description
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) . 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.
Depends
R (>= 3.3.0)
Imports
methods, optparse, data.table (>= 1.11.0), R.utils, ggplot2, ggforce, ggrepel, cowplot, UpSetR, dplyr, sys
Suggests
testthat, knitr, rmarkdown
License
MIT + file LICENSE
SystemRequirements
plink (1.9)
Encoding
UTF-8
LazyData
true
RoxygenNote
6.1.0
VignetteBuilder
knitr
NeedsCompilation
no
Packaged
2019-03-01 21:29:29 UTC; hannah
Author
Hannah Meyer [aut, cre] ()
Repository
CRAN
Date/Publication
2019-03-01 21:50:15 UTC

install.packages('plinkQC')

0.2.1

a month ago

https://github.com/HannahVMeyer/plinkQC

Hannah Meyer

MIT + file LICENSE

Depends on

R (>= 3.3.0)

Imports

methods, optparse, data.table (>= 1.11.0), R.utils, ggplot2, ggforce, ggrepel, cowplot, UpSetR, dplyr, sys

Suggests

testthat, knitr, rmarkdown

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