gl2genalex: Converts a genlight object into a format suitable for input...

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

Converts a genlight object into a format suitable for input to genalex

Description

The output csv file contains the snp data and other relevant lines suitable for genalex. This script is a wrapper for genind2genalex (package poppr).

Usage

gl2genalex(
  x,
  outfile = "genalex.csv",
  outpath = tempdir(),
  overwrite = 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 'genalex.csv'].
outpath	Path where to save the output file [default tempdir()].
overwrite	If FALSE and filename exists, then the file will not be overwritten. Set this option to TRUE to overwrite the file [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].

Value

returns no value (i.e. NULL)

Author(s)

Custodian: Luis Mijangos, Author: Katrin Hohwieler, wrapper Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

References

Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539. http://bioinformatics.oxfordjournals.org/content/28/19/2537

Examples

gl2genalex(testset.gl, outfile='testset.csv')

dartR documentation built on June 8, 2023, 6:48 a.m.