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

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].

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

Author

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

Examples

# \donttest{
gl2genalex(testset.gl, outfile='testset.csv')
#> Starting gl2genalex 
#>   Processing genlight object with SNP data
#> Extracting the table ... Writing the table to /tmp/RtmpMqupE6/testset.csv ... Done.
#> Completed: gl2genalex 
#> 
#> NULL
# }