Estimate individual missingness

Estimate missingness for each individual (i.e. the frequency of missing genotypes in an individual).

Usage

indiv_missingness(.x, as_counts, block_size, ...)

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

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

Arguments

.x

a vector of class vctrs_bigSNP (usually the genotype 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).

block_size

maximum number of loci read at once.

...

currently unused.

Value

a vector of heterozygosities, one per individuals in the gen_tibble

Examples

example_gt <- example_gt("gen_tbl")

example_gt %>% indiv_missingness()
#> [1] 0.0000000 0.1666667 0.1666667 0.0000000 0.0000000 0.1666667 0.1666667

# For missingness as counts:
example_gt %>% indiv_missingness(as_counts = TRUE)
#> [1] 0 1 1 0 0 1 1