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