gl2genepop: Converts a genlight object into genepop format (and file)

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts a genlight object into genepop format (and file)

Description

The genepop format is used by several external applications (for example Neestimator2 (http://www.molecularfisherieslaboratory.com.au/neestimator-software/). So the main idea is to create the genepop file and then run the other software externally. As a feature, the genepop file is also returned as an invisible data.frame by the function.

Usage

gl2genepop(
  x,
  outfile = "genepop.gen",
  outpath = tempdir(),
  pop_order = "alphabetic",
  output_format = "2_digits",
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
outfile	File name of the output file [default 'genepop.gen'].
outpath	Path where to save the output file. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working directory [default tempdir(), mandated by CRAN].
pop_order	Order of the output populations either "alphabetic" or a vector of population names in the order required by the user (see examples) [default "alphabetic"].
output_format	Whether to use a 2-digit format ("2_digits") or 3-digits format ("3_digits") [default "2_digits"].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Value

Invisible data frame in genepop format

Author(s)

Custodian: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

Examples

## Not run: 
require("dartR.data")
# SNP data
geno <- gl2genepop(testset.gl[1:3,1:9])
head(geno)
test <- gl.filter.callrate(platypus.gl,threshold = 1)
popNames(test)
gl2genepop(test, pop_order = c("TENTERFIELD","SEVERN_ABOVE","SEVERN_BELOW"),
           output_format="3_digits")

## End(Not run)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.