utils.get.allele.freq: utils.get.allele.freq

In dartR.popgen: Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

utils.get.allele.freq

Description

Generates percentage allele frequencies by locus and population – This is copy from package dartR function gl.percent.freq

Usage

utils.get.allele.freq(x, verbose = 2)

Arguments

x	Name of the genlight object containing the SNP or Tag P/A (SilicoDArT) data [required].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

This is a support script, to take SNP data or SilicoDArT presence/absence data grouped into populations in a genlight object {adegenet} and generate a table of allele frequencies for each population and locus

Value

A matrix with allele (SNP data) or presence/absence frequencies (Tag P/A data) broken down by population and locus

Author(s)

Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

m <-  utils.get.allele.freq(testset.gl)

dartR.popgen documentation built on March 16, 2026, 9:07 a.m.