Compute the Pairwise Allele Sharing Matrix for a gen_tibble object

This function computes the Allele Sharing matrix. Estimates Allele Sharing (matching in hierfstat)) 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)

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

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.

Value

a matrix of allele sharing between all pairs of individuals