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.
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 https://groups.google.com/d/forum/dartr)
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 #>