gl.percent.freq

-- name of the genlight containing the SNP genotypes or genind object containing the presence/absence data [required]

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]

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

Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

Bernd Gruber

dartR

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

gl.percent.freq: Generate percentage allele frequencies by locus and population

Description

Usage

Arguments

Value

Examples