loci_missingness: Estimate missingness at each locus

In tidypopgen: Tidy Population Genetics

Estimate missingness at each locus

Description

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

Examples

example_gt <- load_example_gt("gen_tbl")

# For missingness
example_gt %>% loci_missingness()

# For missingness per locus per population
example_gt %>%
  group_by(population) %>%
  loci_missingness()
# alternatively, return a list of populations with their missingness
example_gt %>%
  group_by(population) %>%
  loci_missingness(type = "list")
# or a matrix with populations in columns and loci in rows
example_gt %>%
  group_by(population) %>%
  loci_missingness(type = "matrix")
# or within reframe (not recommended, as it much less efficient
# than using it directly as shown above)
example_gt %>%
  group_by(population) %>%
  reframe(missing = loci_missingness(genotypes))

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.