| gl2treemix {dartR.base} | R Documentation |
Converts a genlight object to a treemix input file
Description
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 = NULL, verbose = NULL)
Arguments
x |
Name of the genlight object [required]. |
outfile |
File name of the output file (including gz extension) [default 'treemix_input.gz']. |
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]. |
Value
returns no value (i.e. NULL)
Author(s)
Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)
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
See Also
Other linker:
gl2bayesAss(),
gl2bayescan(),
gl2bpp(),
gl2demerelate(),
gl2eigenstrat(),
gl2faststructure(),
gl2gds(),
gl2genalex(),
gl2genepop(),
gl2geno(),
gl2gi(),
gl2hiphop(),
gl2phylip(),
gl2plink(),
gl2related(),
gl2sa(),
gl2structure(),
gl2vcf()
Examples
gl2treemix(testset.gl, outpath=tempdir())