Compute the Identity by State Matrix for a gen_tibble object

This function computes the IBS matrix.

pairwise_ibs(
  x,
  as_matrix = FALSE,
  type = c("proportion", "adjusted_counts", "raw_counts"),
  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)

type

one of "proportion" (equivalent to "ibs" in PLINK), "adjusted_counts" ("distance" in PLINK), and "raw_counts" (the counts of identical alleles and non-missing alleles, from which the two other quantities are computed)

block_size

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

Value

a bigstatsr::FBM of proportion or adjusted counts, or a list of two bigstatsr::FBM matrices, one of counts of IBS by alleles, and one of number of valid alleles (i.e. 2n_loci - 2missing_loci)

Details

Note that monomorphic sites are currently counted. Should we filter them beforehand? What does plink do?