Compute population specific Fst — pop

This function computes population specific Fst, using the approach in Weir and Goudet 2017 (as computed by hierfstat::fst.dosage()).

Usage

pop_fst(.x, include_global = FALSE, allele_sharing_mat = NULL)

Arguments

.x: a grouped gen_tibble (as obtained by using dplyr::group_by())
include_global: boolean determining whether, besides the population specific Fst, a global Fst should be appended. Note that this will return a vector of n populations plus 1 (the global value)
allele_sharing_mat: optional, the matrix of Allele Sharing returned by pairwise_allele_sharing() with as_matrix=TRUE. As a number of statistics can be derived from the Allele Sharing matrix,

Value

a vector of population specific Fst (plus the global value if include_global=TRUE)

References

Weir, BS and Goudet J (2017) A Unified Characterization of Population Structure and Relatedness. Genetics (2017) 206:2085

Examples

example_gt <- example_gt("grouped_gen_tbl")

# Compute FIS using Nei87
example_gt %>% pop_fst()
#>       pop1       pop2       pop3 
#> 0.05246079 0.06544078 0.41590049 

# To include the global Fst, set include_global = TRUE
example_gt %>% pop_fst(include_global = TRUE)
#>       pop1       pop2       pop3     global 
#> 0.05246079 0.06544078 0.41590049 0.17793402 

# To calculate from a pre-computed allele sharing matrix:
allele_sharing_mat <- pairwise_allele_sharing(example_gt, as_matrix = TRUE)
example_gt %>% pop_fst(allele_sharing_mat = allele_sharing_mat)
#>       pop1       pop2       pop3 
#> 0.05246079 0.06544078 0.41590049