The function converts a genlight object (SNP or presence/absence i.e. SilicoDArT data) into a file in the 'geno' and the 'lfmm' formats from (package LEA).
Usage
gl2geno(x, outfile = "gl_geno", outpath = tempdir(), verbose = NULL)Arguments
- x
Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].
- outfile
File name of the output file [default 'gl_geno'].
- 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, unless specified using gl.set.verbosity].
Author
Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)
Examples
# SNP data
gl2geno(testset.gl)
#> Starting gl2geno
#> Processing genlight object with SNP data
#> Output files: gl_geno.geno.lfmm.
#> Completed: gl2geno
#>
# Tag P/A data
gl2geno(testset.gs)
#> Starting gl2geno
#> Processing genlight object with Presence/Absence (SilicoDArT) data
#> Output files: gl_geno.geno.lfmm.
#> Completed: gl2geno
#>