tidypopgen (version 0.4.3)

pairwise_allele_sharing: Compute the Pairwise Allele Sharing Matrix for a gen_tibble object

Description

This function computes the Allele Sharing matrix. Estimates Allele Sharing (equivalent to the quantity estimated by hierfstat::matching()) between pairs of individuals (for each locus, gives 1 if the two individuals are homozygous for the same allele, 0 if they are homozygous for a different allele, and 1/2 if at least one individual is heterozygous. Matching is the average of these 0, 1/2 and 1s)

Usage

pairwise_allele_sharing(
  x,
  as_matrix = FALSE,
  block_size = bigstatsr::block_size(nrow(x))
)

Value

a matrix of allele sharing between all pairs of individuals

Arguments

x

a gen_tibble object.

as_matrix

boolean, determining whether the results should be a square symmetrical matrix (TRUE), or a tidied tibble (FALSE, the default)

block_size

maximum number of loci read at once. More loci should improve speed, but will tax memory.

See Also

hierfstat::matching()

Examples

example_gt <- load_example_gt("gen_tbl")

# Compute allele sharing between individuals
example_gt %>% pairwise_allele_sharing(as_matrix = FALSE)

# Alternatively, return as a tibble
example_gt %>% pairwise_allele_sharing(as_matrix = TRUE)