Estimate nucleotide diversity (pi) at each locus

Estimate nucleotide diversity (pi) at each locus, accounting for missing values. This uses the formula: c_0 * c_1 / (n * (n-1) / 2)

Usage

loci_pi(.x, .col = "genotypes", n_cores, block_size, type, ...)

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

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

# S3 method for class 'grouped_df'
loci_pi(
  .x,
  .col = "genotypes",
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(nrow(.x), 1),
  type = c("tidy", "list", "matrix"),
  ...
)

Arguments

.x: a vector of class vctrs_bigSNP (usually the genotypes column of a gen_tibble object), or a gen_tibble.
.col: the column to be used when a tibble (or grouped tibble is passed directly to the function). This defaults to "genotypes" and can only take that value. There is no need for the user to set it, but it is included to resolve certain tidyselect operations.
n_cores: number of cores to be used, it defaults to bigstatsr::nb_cores()
block_size: maximum number of loci read at once.
type: type of object to return, if using grouped method. One of "tidy", "list", or "matrix". Default is "tidy".
...: other arguments passed to specific methods, currently unused.

Value

a vector of frequencies, one per locus