Estimate missingness at each locus — loci

Estimate the rate of missingness at each locus.

Usage

loci_missingness(
  .x,
  as_counts = FALSE,
  n_cores = bigstatsr::nb_cores(),
  block_size,
  ...
)

# S3 method for class 'tbl_df'
loci_missingness(
  .x,
  as_counts = FALSE,
  n_cores = n_cores,
  block_size = bigstatsr::block_size(nrow(.x), 1),
  ...
)

# S3 method for class 'vctrs_bigSNP'
loci_missingness(
  .x,
  as_counts = FALSE,
  n_cores = n_cores,
  block_size = bigstatsr::block_size(length(.x), 1),
  ...
)

# S3 method for class 'grouped_df'
loci_missingness(
  .x,
  as_counts = FALSE,
  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.
as_counts: boolean defining whether the count of NAs (rather than the rate) should be returned. It defaults to FALSE (i.e. rates are returned by default).
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.

Value

a vector of frequencies, one per locus