gl2faststructure: Converts a genlight object into faststructure format (to run...

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

Converts a genlight object into 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 [default FALSE].
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.

Value

returns no value (i.e. NULL)

Author(s)

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

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