Estimate Tajima's D for the whole genome

Note that Tajima's D estimates from data that have been filtered or ascertained can be difficult to interpret. This function should ideally be used on sequence data prior to filtering.

Usage

pop_tajimas_d(.x, n_cores, block_size, ...)

# S3 method for class 'tbl_df'
pop_tajimas_d(
  .x,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(nrow(.x), 1),
  ...
)

# S3 method for class 'vctrs_bigSNP'
pop_tajimas_d(
  .x,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(length(.x), 1),
  ...
)

# S3 method for class 'grouped_df'
pop_tajimas_d(
  .x,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(nrow(.x), 1),
  ...
)

Arguments

.x

a vector of class vctrs_bigSNP (usually the genotypes column of a gen_tibble object), or a gen_tibble.

n_cores

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

block_size

maximum number of loci read at once.

...

other arguments passed to specific methods, currently unused.

Value

A single numeric value (Tajima's D D) for the whole data set, NA when the statistic is not defined. For grouped data a list of Tajima's D D values (one per group) is returned.

Examples

example_gt <- example_gt("grouped_gen_tbl")

# Compute Tajima's D
example_gt %>% pop_tajimas_d()
#> [[1]]
#> [1] 1.218829
#> 
#> [[2]]
#> [1] -0.780123
#> 
#> [[3]]
#> [1] 14.90782
#>