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

The output text file contains the SNP data and relevant BAyescan command lines to guide input.

Usage

gl2bayescan(x, outfile = "bayescan.txt", outpath = tempdir(), verbose = NULL)

Arguments

x

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

outfile

File name of the output file (including extension) [default bayescan.txt].

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 or as specified using gl.set.verbosity].

References

Foll M and OE Gaggiotti (2008) A genome scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics 180: 977-993.

Author

Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

Examples

out <- gl2bayescan(testset.gl)
#> Starting gl2bayescan 
#>   Processing genlight object with SNP data
#> Extracting SNP data and creating records for each individual
#> 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 text input file for Bayescan /tmp/RtmpMqupE6/bayescan.txt 
#> Completed: gl2bayescan 
#>