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Generates percentage allele frequencies by locus and population

Source: R/gl.percent.freq.r
gl.percent.freq.Rd

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

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

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

Examples

m <-  gl.percent.freq(testset.gl)
#> Starting gl.percent.freq 
#>   Processing genlight object with SNP data
#> Warning: Monomorphic loci retained, used in calculations
#> Starting gl.percent.freq: Calculating allele frequencies for populations
#> Completed: gl.percent.freq 
#>