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Compute pairwise Fst for a sliding window

Source: R/windows_pairwise_pop_fst.R
windows_pairwise_pop_fst.Rd

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
)

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.

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

Examples

example_gt <- 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
  )
#> # A tibble: 3 × 6
#>   chromosome start   end fst_pop1.pop2 fst_pop1.pop3 fst_pop2.pop3
#>   <chr>      <dbl> <dbl>         <dbl>         <dbl>         <dbl>
#> 1 chr1           1     3         0.277         0.311           0.4
#> 2 chr1           3     5        -0.167         0.222           0  
#> 3 chr2           1     3        -0.16         -0.467          -0.5