checkPlink2

checkPlink checks that the PLINK software version 2.0
(<a href="https://www.cog-genomics.org/plink/2.0/">https://www.cog-genomics.org/plink/2.0/</a>)
can be found from system call.

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. Additionally, there is a trained classifier to predict
genomic ancestry of human samples.

Hannah Meyer

plinkQC

Genotype Quality Control with 'PLINK'

Caroline Walter

Maha Syed

checkPlink2 function

<dl><dt>path2plink2</dt>
<dd>[character] Absolute path to PLINK executable
(<a href="https://www.cog-genomics.org/plink/2.0/">https://www.cog-genomics.org/plink/2.0/</a>) i.e.
plink 2 should be accessible as path2plink -h. The full name of the executable
should be specified: for windows OS, this means path/plink.exe, for unix
platforms this is path/plink. If not provided, assumed that PATH set-up works
and PLINK will be found by <code><a href="/link/exec?package=plinkQC&version=1.0.0" data-mini-rdoc="plinkQC::exec">exec</a></code>('plink').</dd></dl>

Arguments

checkPlink checks that the PLINK software version 2.0
(<a href='https://www.cog-genomics.org/plink/2.0/'>https://www.cog-genomics.org/plink/2.0/</a>)
can be found from system call.

Check PLINK2 software access — checkPlink2

<dl>

<dt>path2plink2</dt>
<dd>[character] Absolute path to PLINK executable
(<a href='https://www.cog-genomics.org/plink/2.0/'>https://www.cog-genomics.org/plink/2.0/</a>) i.e.
plink 2 should be accessible as path2plink -h. The full name of the executable
should be specified: for windows OS, this means path/plink.exe, for unix
platforms this is path/plink. If not provided, assumed that PATH set-up works
and PLINK will be found by <code><a href='https://rdrr.io/pkg/sys/man/exec.html'>exec</a></code>('plink').</dd>

</dl>

checkPlink2: Check PLINK2 software access

Description

Usage

Value

Arguments