gl2treemix: Converts a genlight object to a treemix input file

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

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())

dartR.base documentation built on April 4, 2025, 2:45 a.m.