tidypopgen (version 0.4.3)

pairwise_pop_fst: Compute pairwise population Fst

Description

This function computes pairwise Fst. The following methods are implemented:

• 'Hudson': Hudson's formulation, as derived in Bhatia et al (2013) for diploids. This is the only method that can also be used with pseudohaploid data.

• 'Nei87' : Fst according to Nei (1987) - includes the correction for heterozygosity when computing Ht (it uses the same formulation as in hierfstat::pairwise.neifst()),

• 'WC84' : Weir and Cockerham (1984), correcting for missing data (it uses the same formulation as in hierfstat::pairwise.WCfst()).

Usage

pairwise_pop_fst(
  .x,
  type = c("tidy", "pairwise"),
  by_locus = FALSE,
  by_locus_type = c("tidy", "matrix", "list"),
  method = c("Hudson", "Nei87", "WC84"),
  return_num_dem = FALSE,
  n_cores = bigstatsr::nb_cores()
)

Value

if type=tidy, a tibble of genome-wide pairwise Fst values with each pairwise combination as a row if "by_locus=FALSE", else a list including the tibble of genome-wide values as well as a matrix with pairwise Fst by locus with loci as rows and and pairwise combinations as columns. If type=pairwise, a matrix of genome-wide pairwise Fst values is returned.

Arguments

.x

a grouped gen_tibble (as obtained by using dplyr::group_by())

type

type of object to return One of "tidy" or "pairwise" for a pairwise matrix of populations. Default is "tidy".

by_locus

boolean, determining whether Fst should be returned by locus(TRUE), or as a single genome wide value obtained by taking the ratio of the mean numerator and denominator (FALSE, the default).

by_locus_type

type of object to return. One of "tidy", "matrix" or "list". Default is "tidy".

method

one of 'Hudson', 'Nei87', and 'WC84'

return_num_dem

returns a list of numerators and denominators for each locus. This is useful for creating windowed estimates of Fst (as we need to compute the mean numerator and denominator within each window). Default is FALSE.

n_cores

number of cores to be used, it defaults to bigstatsr::nb_cores()

Details

For all formulae, the genome wide estimate is obtained by taking the ratio of the mean numerators and denominators over all relevant SNPs.

References

Bhatia G, Patterson N, Sankararaman S, Price AL. (2013) Estimating and Interpreting FST: The Impact of Rare Variants. Genome Research, 23(9):1514–1521.

Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press

Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 38(6): 1358–1370.

See Also

hierfstat::pairwise.neifst()

Examples

if (FALSE) { # all(rlang::is_installed(c("RhpcBLASctl", "data.table")))
# \dontshow{
data.table::setDTthreads(2)
RhpcBLASctl::blas_set_num_threads(2)
RhpcBLASctl::omp_set_num_threads(2)
# }
example_gt <- load_example_gt("gen_tbl")

# For a basic global pairwise Fst calculation:
example_gt %>%
  group_by(population) %>%
  pairwise_pop_fst(method = "Nei87")

# With a pairwise matrix:
example_gt %>%
  group_by(population) %>%
  pairwise_pop_fst(method = "Nei87", type = "pairwise")

# To calculate Fst by locus:
example_gt %>%
  group_by(population) %>%
  pairwise_pop_fst(method = "Hudson", by_locus = TRUE)
}