calculateAlleleFreqs

This function calculates allele frequencies from a genotype matrix (sep_gt) for each variant.
It is designed to be used within the batch or window processing framework of <code>process_vcf_in_batches</code> and <code>process_vcf_in_windows</code>.

internal

Tools for efficient processing of large, whole genome genotype data sets in variant call format (VCF). It includes several functions to calculate commonly used population genomic metrics and a method for reference panel free genotype imputation, which is described in the preprint Gurke & Mayer (2024) <doi:10.22541/au.172515591.10119928/v1>.

Marie Gurke

GenoPop

Genotype Imputation and Population Genomics Efficiently from
Variant Call Formatted (VCF) Files

calculateAlleleFreqs function

<dl><dt>sep_gt</dt>
<dd>Genotype matrix similar to the <code>@sep_gt</code> slot of a <code>vcfR</code> object.</dd></dl>

Arguments

Calculate Allele Frequencies from Genotype Matrix — calculateAlleleFreqs

<dl>

<dt>sep_gt</dt>
<dd>Genotype matrix similar to the <code>@sep_gt</code> slot of a <code>vcfR</code> object.</dd>

</dl>

calculateAlleleFreqs: Calculate Allele Frequencies from Genotype Matrix

Description

Usage

Value

Arguments