gl2sfs: Converts a genlight object into a sfs input 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 a sfs input file

Description

The output of this function is suitable for analysis in fastsimcoal2 or dada.

Usage

gl2sfs(
  x,
  n.invariant.tags = 0,
  outfile_root = "gl2sfs",
  outpath = tempdir(),
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
n.invariant.tags	Number of invariant sites[default 0].
outfile_root	The root of the name of the output file [default "gl2sfs"].
outpath	Path where to save the output file [default 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, unless specified using gl.set.verbosity].

Details

It saves a derived sfs, assuming that the reference allele is the ancestral, and a MAF sfs.

At this stage this function caters only for diploid organisms, for samples from one population only, and for genotypes without missing data. Note that sfs uses frequencies considered independent, data are assumed to be from independent (i.e. not linked) loci. This means that only one site per tag should be considered 9i.e. secondaries should be removed). If no monomorphic site estimates is provided (with n.invariant.tags), the sfs will only include the number of monomorphic sites in the data (but this will be a biased estimates as it doesn't take into account the invariant tags that have not been included. This will affect parameter estimates in the analyses). Note that the number of invariant tags can be estimated with gl.report.secondaries. In a limited number of cases, ascertainment bias can be explicitly modelled in fastsimcoal2. See fastsimcoal2 manual for details.

It expects a dartR formatted genlight object, but it should also work with other genlight objects.

Value

Deprecated. Please use gl.sfs instead.

Author(s)

Custodian: Carlo Pacioni (Post to https://groups.google.com/d/forum/dartr)

References

Excoffier L., Dupanloup I., Huerta-Sánchez E., Sousa V. C. and Foll M. (2013) Robust demographic inference from genomic and SNP data. PLoS genetics 9(10)

See Also

gl.report.heterozygosity, gl.report.secondaries, utils.n.var.invariant

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