gl.allele.freq {dartR.base}

Generates percentage allele frequencies by locus and population

Description

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.allele.freq(x, percent = FALSE, by = "pop", simple = FALSE, verbose = NULL)

Arguments

x

Name of the genlight object containing the SNP or Tag P/A (SilicoDArT) data [required].

percent

If TRUE, percentage allele frequencies are given, if FALSE allele proportions are given [default FALSE]

by

If by='popxloc' then breakdown is given by population and locus; if by='pop' then breakdown is given by population with statistics averaged across loci; if by='loc' then breakdown is given by locus with statistics averaged across individuals [default 'pop']

simple

A legacy option to return a dataframe with the frequency of the reference allele (alf1) and the frequency of the alternate allele (alf2) by locus [default FALSE]

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)

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

See Also

Other unmatched report: gl.report.basics(), gl.report.diversity(), gl.report.heterozygosity()

Examples

gl.allele.freq(testset.gl,percent=FALSE,by='pop')
gl.allele.freq(testset.gl,percent=FALSE,by="loc")
gl.allele.freq(testset.gl,percent=FALSE,by="popxloc")
gl.allele.freq(testset.gl,simple=TRUE)