gl2svdquartets: Converts a genlight object to nexus format PAUP SVDquartets

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

Converts a genlight object to nexus format PAUP SVDquartets

Description

The output nexus file contains the SNP data in one of two forms, depending upon what you regard as most appropriate. One form, that used by Chifman and Kubatko, has two lines per individual, one providing the reference SNP the second providing the alternate SNP (method=1).

Usage

gl2svdquartets(
  x,
  outfile = "svd.nex",
  outpath = tempdir(),
  method = 2,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data or tag P/A data [required].
outfile	File name of the output file (including extension) [default 'svd.nex'].
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.
method	Method = 1, nexus file with two lines per individual; method = 2, nexus file with one line per individual, ambiguity codes for SNP genotypes, 0 or 1 for presence/absence data [default 2].
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]

Details

A second form, recommended by Dave Swofford, has a single line per individual, resolving heterozygous SNPs by replacing them with standard ambiguity codes (method=2).

If the data are tag presence/absence, then method=2 is assumed.

Note that the genlight object must contain at least two populations for this function to work.

Value

returns no value (i.e. NULL)

Author(s)

Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

References

Chifman, J. and L. Kubatko. 2014. Quartet inference from SNP data under the coalescent. Bioinformatics 30: 3317-3324

Examples

gg <- testset.gl[1:20,1:100]
gg@other$loc.metrics <- gg@other$loc.metrics[1:100,]
gl2svdquartets(gg)

green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.