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Compute pairwise Fst with block jackknife standard errors

Source: R/jackknife_pairwise_pop_fst.R
jackknife_pairwise_pop_fst.Rd

This function computes genome-wide pairwise Fst, together with its standard error estimated with a weighted block jackknife.

Usage

jackknife_pairwise_pop_fst(.x, ...)

# S3 method for class 'gen_tbl'
jackknife_pairwise_pop_fst(
  .x,
  type = c("matrix", "tidy"),
  method = c("Hudson", "Nei87", "WC84"),
  block_size,
  size_unit = c("snp", "cM", "bp"),
  ...
)

Arguments

.x

a grouped gen_tibble object. If grouped by more than one variable, groups are labelled by the values of the grouping variables pasted with "." (e.g. pop1.F).

...

other arguments passed to specific methods, currently unused.

type

type of object to return. One of "matrix" or "tidy". Default is "matrix". "matrix" returns a dataframe where each row is a quantity (estimate, jack_estimate, se, z and n_blocks), followed by columns for each pairwise population a and b comparison. "tidy" returns a tidy tibble where each row is 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.

block_size

The size of the blocks to leave out.

size_unit

Either "snp", "cM" or "bp". If "snp", the block size is in number of SNPs. If "cM", the block size is in centiMorgans. If "bp", the block size is in base pairs.

Value

either a data frame with the following columns:

  • quantity: the quantity reported in the row, one of estimate (Fst computed on all loci), jack_estimate (the bias corrected jackknife estimate), se (the jackknife standard error), z (jack_estimate/se), and n_blocks (the number of blocks used)

  • fst_a.b: the values for the pairwise Fst between 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:

  • stat_name: the name of population a and b used in the pairwise Fst calculation (e.g. "fst_pop1.pop2")

  • estimate, jack_estimate, se, z, n_blocks: as described above

Details

The genome is divided into non-overlapping blocks, which never span more than one chromosome, and Fst is recomputed leaving out one block at a time. The standard error is computed with the weighted delete-m jackknife of Busing et al. (1999), where each block is weighted by the number of loci it contains. Fst is computed as the ratio of the sum of the per locus numerators and denominators, so leaving out a block is achieved by subtracting its sums, without having to rescan the genotypes. See jackknife_stats_generic() for details.

References

Busing FMTA, Meijer E, Van Der Leeden R (1999) Delete-m jackknife for unequal m. Statistics and Computing 9:3-8.

Examples

example_gt <- load_example_gt("gen_tbl")

example_gt %>%
  group_by(population) %>%
  jackknife_pairwise_pop_fst(
    block_size = 2,
    size_unit = "snp"
  )
#> # A tibble: 5 × 4
#>   quantity      fst_pop1.pop2 fst_pop1.pop3 fst_pop2.pop3
#>   <chr>                 <dbl>         <dbl>         <dbl>
#> 1 estimate             0.0345        0.0556         0    
#> 2 jack_estimate        0.0626        0.0698         0    
#> 3 se                   0.185         0.286          0.385
#> 4 z                    0.338         0.244          0    
#> 5 n_blocks             3             3              3