dartR: gl2treemix – R documentation

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gl2treemix

Convert 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 = tempdir(),
  verbose = NULL
)

Arguments

`x`	– name of the genlight object containing the SNP data [required]
`outfile`	– file name of the output file (including gz extension)[default treemix_input.gz]
`outpath`	– path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() when calling this function or set.tempdir <- getwd() elsewhere in your script to direct output files to your working directory.
`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(s)

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

Examples

gl2treemix(testset.gl, outpath=tempdir())

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29