gl.sfs: Creates a site frequency spectrum based on a dartR or...

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

Creates a site frequency spectrum based on a dartR or genlight object

Description

Creates a site frequency spectrum based on a dartR or genlight object

Usage

gl.sfs(
  x,
  minbinsize = 0,
  folded = TRUE,
  singlepop = FALSE,
  plot.out = TRUE,
  verbose = NULL
)

Arguments

x	dartR/genlight object
minbinsize	remove bins from the left of the sfs. For example to remove singletons (alleles only occurring once among all individuals) set minbinsize to 2. If set to zero, also monomorphic (d0) loci are returned.
folded	if set to TRUE (default) a folded sfs (minor allele frequency sfs) is returned. If set to FALSE then an unfolded (derived allele frequency sfs) is returned. It is assumed that 0 is homozygote for the reference and 2 is homozygote for the derived allele. So you need to make sure your coding is correct.
singlepop	switch to force to create a one-dimensional sfs, even though the genlight/dartR object contains more than one population
plot.out	Specify if plot is to be produced [default TRUE].
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

returns a site frequency spectrum, either a one dimensional vector (only a single population in the dartR/genlight object or singlepop=TRUE) or an n-dimensional array (n is the number of populations in the genlight/dartR object). If the dartR/genlight object consists of several populations the multidimensional site frequency spectrum for each population is returned [=a multidimensional site frequency spectrum]. Be aware the multidimensional spectrum works only for a limited number of population and individuals [if too high the table command used internally will through an error as the number of populations and individuals (and therefore dimensions) are too large]. To get a single sfs for a genlight/dartR object with multiple populations, you need to set singlepop to TRUE. The returned sfs can be used to analyse demographics, e.g. using fastsimcoal2.

Author(s)

Custodian: Bernd Gruber & 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)

Examples

gl.sfs(bandicoot.gl, singlepop=TRUE)
gl.sfs(possums.gl[c(1:5,31:33),], minbinsize=1)

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