gl2genalex

-- name of the genlight object containing the SNP data [required]

-- file name of the output file (including extension) [default 'genalex.csv']

outfile

-- path where to save the output file [default tempdir()]

outpath

-- 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]

verbose

The output csv file contains the snp data and other relevant lines suitable for genalex. This script is a wrapper for genind2genalex poppr

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

gl2genalex: Convert a genlight object to format suitable for input to genalex

Description

Usage

Arguments

Details

Examples