tidypopgen (version 0.4.3)

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

Value

a vector of frequencies, one per locus

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.

Examples

if (FALSE) { # all(rlang::is_installed(c("RhpcBLASctl", "data.table")))
# \dontshow{
data.table::setDTthreads(2)
RhpcBLASctl::blas_set_num_threads(2)
RhpcBLASctl::omp_set_num_threads(2)
# }
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))
}