Converts a genlight object to STRUCTURE formated files
gl2structure.RdThis 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.
Usage
gl2structure(
x,
indNames = NULL,
addcolumns = NULL,
ploidy = 2,
exportMarkerNames = TRUE,
outfile = "gl.str",
outpath = tempdir(),
verbose = NULL
)Arguments
- 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].