dartR.base (version 1.0.5)

gl2bayesAss: Converts a genlight object into bayesAss (BA3) input format

Description

This function exports a genlight object into bayesAss format and save it into a file. This function only caters for ploidy=2.

Usage

gl2bayesAss(
  x,
  ploidy = 2,
  outfile = "gl.BayesAss.txt",
  outpath = NULL,
  verbose = NULL
)

Value

returns the input file as data.table

Arguments

x

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

ploidy

Set the ploidy [defaults 2].

outfile

File name of the output file [default 'gl.BayesAss.txt'].

outpath

Path where to save the output file [default global working directory or if not specified, tempdir()].

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].

Author

Custodian: Carlo Pacioni (Post to https://groups.google.com/d/forum/dartr)

References

Mussmann S. M., Douglas M. R., Chafin T. K. and Douglas M. E. (2019) BA3-SNPs: Contemporary migration reconfigured in BayesAss for next-generation sequence data. Methods in Ecology and Evolution 10, 1808-1813.

Wilson G. A. and Rannala B. (2003) Bayesian Inference of Recent Migration Rates Using Multilocus Genotypes. Genetics 163, 1177-1191.

See Also

Other linker: gl2bayescan(), gl2bpp(), gl2demerelate(), gl2eigenstrat(), gl2faststructure(), gl2gds(), gl2genalex(), gl2genepop(), gl2geno(), gl2gi(), gl2hiphop(), gl2phylip(), gl2plink(), gl2related(), gl2sa(), gl2structure(), gl2treemix(), gl2vcf()

Examples

require("dartR.data")
#only the first 100 due to check time
gl2bayesAss(platypus.gl[,1:100], outpath=tempdir())