gl2structure: Converts a genlight object to STRUCTURE formatted files

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts a genlight object to STRUCTURE formatted files

Description

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.

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].

Value

returns no value (i.e. NULL)

Author(s)

Bernd Gruber (wrapper) and Lindsay V. Clark [[e-mail]]

Examples

#not run here
#gl2structure(testset.gl)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.