tidypopgen (version 0.4.3)

loci_alt_freq: Estimate allele frequencies at each locus

Description

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. Both loci_maf() and loci_alt_freq() have efficient methods to support grouped gen_tibble objects. These can return a tidied tibble, a list, or a matrix.

Usage

loci_alt_freq(
  .x,
  .col = "genotypes",
  as_counts = FALSE,
  n_cores,
  block_size,
  type,
  ...
)
# S3 method for tbl_df
loci_alt_freq(
  .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_alt_freq(
  .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_alt_freq(
  .x,
  .col = "genotypes",
  as_counts = FALSE,
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(nrow(.x), 1),
  type = c("tidy", "list", "matrix"),
  ...
)
loci_maf(.x, .col = "genotypes", n_cores, block_size, type, ...)
# S3 method for tbl_df
loci_maf(
  .x,
  .col = "genotypes",
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(nrow(.x), 1),
  ...
)
# S3 method for vctrs_bigSNP
loci_maf(
  .x,
  .col = "genotypes",
  n_cores = bigstatsr::nb_cores(),
  block_size = bigstatsr::block_size(length(.x), 1),
  ...
)
# S3 method for grouped_df
loci_maf(
  .x,
  .col = "genotypes",
  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, if as_counts = FALSE; else a matrix of two columns, the count of alternate alleles and the count valid alleles (i.e. the sum of alternate and reference)

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 alternate and valid (i.e. total number) alleles (rather than the frequencies) should be returned. It defaults to FALSE (i.e. frequencies 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, currently unused.

Examples

# \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 alternate allele frequency
example_gt %>% loci_alt_freq()

# For alternate allele frequency per locus per population
example_gt %>%
  group_by(population) %>%
  loci_alt_freq()
# alternatively, return a list of populations with their frequencies
example_gt %>%
  group_by(population) %>%
  loci_alt_freq(type = "list")
# or a matrix with populations in columns and loci in rows
example_gt %>%
  group_by(population) %>%
  loci_alt_freq(type = "matrix")
# or within reframe (not recommended, as it much less efficient
# than using it directly as shown above)
library(dplyr)
example_gt %>%
  group_by(population) %>%
  reframe(alt_freq = loci_alt_freq(genotypes))
# For MAF
example_gt %>% loci_maf()

# For minor allele frequency per locus per population
example_gt %>%
  group_by(population) %>%
  loci_maf()
# alternatively, return a list of populations with their frequencies
example_gt %>%
  group_by(population) %>%
  loci_maf(type = "list")
# or a matrix with populations in columns and loci in rows
example_gt %>%
  group_by(population) %>%
  loci_maf(type = "matrix")