Estimate missingness at each locus

Estimate the rate of missingness at each locus. This function has an efficient method to support grouped gen_tibble objects, which can return a tidied tibble, a list, or a matrix.

Usage

loci_missingness(
  .x,
  .col = "genotypes",
  as_counts = FALSE,
  n_cores = bigstatsr::nb_cores(),
  block_size,
  type,
  ...
)

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

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

# S3 method for class 'grouped_df'
loci_missingness(
  .x,
  .col = "genotypes",
  as_counts = FALSE,
  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.
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.
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.

Value

a vector of frequencies, one per locus

Usage

Arguments

Value

Examples