dartR: gl2genalex – R documentation

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gl2genalex

Convert a genlight object to format suitable for input to genalex

Description

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

Usage

gl2genalex(x, outfile = "genalex.csv", outpath = tempdir(), verbose = NULL)

Arguments

`x`	– name of the genlight object containing the SNP data [required]
`outfile`	– file name of the output file (including extension) [default 'genalex.csv']
`outpath`	– path where to save the output file [default tempdir()]
`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]

Details

Reference: Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539. http://bioinformatics.oxfordjournals.org/content/28/19/2537

Author(s)

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

Examples

gl2genalex(testset.gl, outfile="testset.csv")

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