gl2structure {dartR.base}

Converts a genlight object to STRUCTURE formatted files

Description

This function exports genlight objects to STRUCTURE formatted files (be aware there is a gl2faststructure version as well). It is based on the code provided by Lindsay Clark (see https://github.com/lvclark/R_genetics_conv) and this function is basically a wrapper around her numeric2structure function. See also: Lindsay Clark. (2017, August 22). lvclark/R_genetics_conv: R_genetics_conv 1.1 (Version v1.1). Zenodo: doi.org/10.5281/zenodo.846816.

Usage

gl2structure(
  x,
  ind.names = NULL,
  add.columns = NULL,
  ploidy = 2,
  export.marker.names = TRUE,
  outfile = "gl.str",
  outpath = NULL,
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP data and location data, lat longs [required].

ind.names

Specify individuals names to be added [if NULL, defaults to ind.names(x)].

add.columns

Additional columns to be added before genotypes [default NULL].

ploidy

Set the ploidy [defaults 2].

export.marker.names

If TRUE, locus names locNames(x) will be included [default TRUE].

outfile

File name of the output file (including extension) [default "gl.str"].

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)

Bernd Gruber (wrapper) and Lindsay V. Clark [[e-mail]]; Custodian Bernd Gruber

See Also

Other linker: gl2bayesAss(), gl2bayescan(), gl2bpp(), gl2demerelate(), gl2eigenstrat(), gl2faststructure(), gl2gds(), gl2genalex(), gl2genepop(), gl2geno(), gl2gi(), gl2hiphop(), gl2phylip(), gl2plink(), gl2related(), gl2sa(), gl2treemix(), gl2vcf()

Examples

gl2structure(testset.gl[1:10,1:50], outpath=tempdir())