vcf2pcadapt

<code>vcf2pcadapt</code> uses the package <code>vcfR</code> to extract the genotype information 
from a vcf file and exports it under the format required by <code>pcadapt</code>.
Note that this VCF converter is not maintained anymore. Please use PLINK.

internal

Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis. Implements the method described in (Luu, 2016)
<DOI:10.1111/1755-0998.12592> and later revised in (Privé, 2020)
<DOI:10.1093/molbev/msaa053>.

Florian Privé

pcadapt

Fast Principal Component Analysis for Outlier Detection

Keurcien Luu

Michael Blum

Eric Bazin

Nicolas Duforet-Frebourg

vcf2pcadapt function

<dl><dt>input</dt>
<dd>a character string specifying the name of the file to be converted.</dd>
<dt>output</dt>
<dd>a character string indicating the name of the output file.</dd>
<dt>allele.sep</dt>
<dd>a vector of characters indicating what delimiters are used
to separate alleles.</dd></dl>

Arguments

vcfR-based converter — vcf2pcadapt

<dl>

<dt>input</dt>
<dd>a character string specifying the name of the file to be converted.</dd>


<dt>output</dt>
<dd>a character string indicating the name of the output file.</dd>


<dt>allele.sep</dt>
<dd>a vector of characters indicating what delimiters are used
to separate alleles.</dd>

</dl>

vcf2pcadapt: vcfR-based converter

Description

Usage

Arguments