tidypopgen (version 0.4.3)

pop_fst: Compute population specific Fst

Description

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)

Value

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

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,

References

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

See Also

hierfstat::fst.dosage()

Examples

example_gt <- load_example_gt("grouped_gen_tbl")

# Compute FIS using Nei87
example_gt %>% pop_fst()

# To include the global Fst, set include_global = TRUE
example_gt %>% pop_fst(include_global = TRUE)

# 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)