Estimate allele frequencies at each each locus — loci_alt

Allele frequencies can be estimates as minimum allele frequencies (MAF) with loci_maf() or the frequency of the alternate allele (with loci_alt_freq()). The latter are in line with the genotypes matrix (e.g. as extracted by show_loci()). Most users will be in interested in the MAF, but the raw frequencies might be useful when computing aggregated statistics.

Usage

loci_alt_freq(.x, n_cores, block_size, ...)

# S3 method for class 'tbl_df'
loci_alt_freq(
  .x,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(nrow(.x), 1),
  ...
)

# S3 method for class 'vctrs_bigSNP'
loci_alt_freq(
  .x,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(length(.x), 1),
  ...
)

# S3 method for class 'grouped_df'
loci_alt_freq(
  .x,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(nrow(.x), 1),
  ...
)

loci_maf(.x, n_cores, block_size, ...)

# S3 method for class 'tbl_df'
loci_maf(
  .x,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(nrow(.x), 1),
  ...
)

# S3 method for class 'vctrs_bigSNP'
loci_maf(
  .x,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(length(.x), 1),
  ...
)

# S3 method for class 'grouped_df'
loci_maf(
  .x,
  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.
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, currently unused.

Value

a vector of frequencies, one per locus