dartR (version 1.1.11)

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 needs to be gzipped before it will be recognised by treemix. Plotting functions can be obtained using source("C:/workspace/R/dartR/R/plotting_funcs.R").

Usage

gl2treemix(x, outfile = "treemix_input.gz", outpath = tempdir(),
  v = 2)

Arguments

x

-- name of the genlight object containing the SNP data [required]

outfile

-- file name of the output file (including extension).

outpath

-- path where to save the output file (set to tempdir by default)

v

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]

Details

Reference: 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

# NOT RUN {
gl2treemix(testset.gl)
# }