Converts genlight objects to STRUCTURE formated files
This function exports genlight objects to STRUCTURE formatted files (be aware there is a gl2faststructure version as well). It is based on the code provided by Lindsay Clark (see https://github.com/lvclark/R_genetics_conv) and this function is basically a wrapper around her numeric2structure function. See also: Lindsay Clark. (2017, August 22). lvclark/R_genetics_conv: R_genetics_conv 1.1 (Version v1.1). Zenodo: doi.org/10.5281/zenodo.846816.
gl2structure( x, indNames = NULL, addcolumns = NULL, ploidy = 2, exportMarkerNames = TRUE, outfile = "gl.str", outpath = tempdir(), verbose = NULL )
x |
– name of the genlight object containing the SNP data and location data, lat longs [required] |
indNames |
– specify individuals names to be added [if NULL, defaults to indNames(x)] |
addcolumns |
– additional columns to be added before genotypes [default NULL] |
ploidy |
– set the ploidy [defaults 2] |
exportMarkerNames |
– if TRUE, locus names locNames(x) will be included [default TRUE] |
outfile |
– file name of the output file (including extension) [default gl.str] |
outpath |
– path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() or outpath="." when calling this function to direct output files to your working directory. |
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] |
Bernd Gruber (wrapper) and Lindsay V. Clark [lvclark@illinois.edu]
#not run here #gl2structure(testset.gl)
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