Converts a genlight object to a treemix input file

The output file contains the SNP data in the format expected by treemix -- see the treemix manual. The file will be gzipped before in order to be recognised by treemix. Plotting functions provided with treemix will need to be sourced from the treemix download page.

Usage

gl2treemix(
  x,
  outfile = "treemix_input.gz",
  outpath = tempdir(),
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP data [required].

outfile

File name of the output file (including gz extension) [default 'treemix_input.gz'].

outpath

Path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() when calling this function or set.tempdir <- getwd() elsewhere in your script 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 or as specified using gl.set.verbosity].

References

Pickrell and Pritchard (2012). Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics https://doi.org/10.1371/journal.pgen.1002967

Author

Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

gl2treemix(testset.gl, outpath=tempdir())
#> Starting gl2treemix 
#>   Processing genlight object with SNP data
#> Starting gl.percent.freq 
#>   Processing genlight object with SNP data
#> Warning: Monomorphic loci retained, used in calculations
#> Starting gl.percent.freq: Calculating allele frequencies for populations
#> Completed: gl.percent.freq 
#>     Writing results to treemix input file /tmp/RtmpMqupE6/treemix_input.gz 
#> Completed: gl2treemix 
#> Output file has been gzipped for input to treemix
#> 
#> NULL