sfs: Site Frequency Spectrum
In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

sfs	R Documentation

Site Frequency Spectrum

Calculate the SFS from a data frame of SNP genotypes

sfs(
  x,
  strata.col = 2,
  locus.col = 3,
  fsc.dimnames = TRUE,
  sort.strata = TRUE,
  na.action = c("fail", "filter")
)

`x`	a data frame of SNP genotypes where the first two columns are id and strata designations and SNPs start on the third column. SNP genotypes are coded as integers where 0 and 2 are the major and minor homozygotes and 1 is the heterozygote.
`strata.col`	column number that strata designations are in.
`locus.col`	column number that loci start in. All columns after this are assumed to be loci.
`fsc.dimnames`	format matrix dimnames for fastsimcoal2? If `TRUE`, then row and column names will be prefixed with the deme number (e.g., "d0_") that they represent.
`sort.strata`	if `joint = TRUE`, are strata to be sorted alphabetically? If `FALSE` then strata are taken in the order found in `strata.col`.
`na.action`	action to take if genotypes are missing for some samples. If `"fail"`, an error is thrown if any genotypes are missing. If `"filter"`, SNPs with missing genotypes are removed.