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


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



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


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


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.


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].


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.


Custodian: Luis Mijangos (Post to


out <- gl2bayescan(
#> 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