vcf_convert

<code>vcf_convert</code> converts outputs of <code>extract.gt</code> to the format 
<code>pcadapt</code>.

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

vcf_convert function

<dl><dt>string_geno</dt>
<dd>a genotype matrix extracted from a VCF file with `vcfR`.</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

Convert vcfR genotype matrices — vcf_convert

<dl>

<dt>string_geno</dt>
<dd>a genotype matrix extracted from a VCF file with `vcfR`.</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>

vcf_convert: Convert vcfR genotype matrices

Description

Usage

Arguments