dartR: gl2faststructure – R documentation

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gl2faststructure

Export DArT genlight object {adegenet} to faststructure format (to run faststructure elsewhere)

Description

Recodes in the quite specific faststructure format (e.g first six columns need to be there, but are ignored...check faststructure documentation (if you find any :-( )))

Usage

gl2faststructure(
  x,
  outfile = "gl.str",
  outpath = tempdir(),
  probar = FALSE,
  verbose = NULL
)

Arguments

`x`	– name of the genlight object containing the SNP data [required]
`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.
`probar`	switch to show/hide progress bar
`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

The script writes out the a file in faststructure format.

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

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