windows_pairwise_pop_fst: Compute pairwise Fst for a sliding window

Description

This function computes pairwise Fst for a sliding window across each chromosome.

Usage

windows_pairwise_pop_fst(
  .x,
  type = c("matrix", "tidy"),
  method = c("Hudson", "Nei87", "WC84"),
  window_size,
  step_size,
  size_unit = c("snp", "bp"),
  min_loci = 1,
  complete = FALSE
)

Value

either a data frame with the following columns:

chromosome: the chromosome for the window
start: the starting locus of the window
end: the ending locus of the window
fst_a.b: the pairwise Fst value for the population a and b (there will be multiple such columns if there are more than two populations) or a tidy tibble with the following columns:
chromosome: the chromosome for the window
start: the starting locus of the window
end: the ending locus of the window
stat_name: the name of population a and b used in the pairwise Fst calculation (e.g. "fst_pop1.pop2")
value: the pairwise Fst value for the population a and b

Arguments

.x: a grouped gen_tibble object
type: type of object to return. One of "matrix" or "tidy". Default is "matrix". "matrix" returns a dataframe where each row is a window, followed by columns of Fst values for each pairwise population a and b comparison. "tidy" returns a tidy tibble of the same data in 'long' format, where each row is one window for one pairwise population a and b comparison.
method: the method to use for calculating Fst, one of 'Hudson', 'Nei87', and 'WC84'. See pairwise_pop_fst() for details.
window_size: The size of the window to use for the estimates.
step_size: The step size to use for the windows.
size_unit: Either "snp" or "bp". If "snp", the window size and step size are in number of SNPs. If "bp", the window size and step size are in base pairs.
min_loci: The minimum number of loci required to calculate a window statistic. If the number of loci in a window is less than this, the window statistic will be NA.
complete: Should the function be evaluated on complete windows only? If FALSE, the default, then partial computations will be allowed at the end of the chromosome.

Examples

Run this code

example_gt <- load_example_gt("gen_tbl")

example_gt %>%
  group_by(population) %>%
  windows_pairwise_pop_fst(
    window_size = 3, step_size = 2,
    size_unit = "snp", min_loci = 2
  )

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