dartR: gl.percent.freq – R documentation

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gl.percent.freq

Generate percentage allele frequencies by locus and population

Description

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

Usage

gl.percent.freq(x, verbose = NULL)

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]

Value

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

Author(s)

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

Examples

m <-  gl.percent.freq(testset.gl)
m

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29