tidypopgen (version 0.4.3)

pairwise_ibs: Compute the Identity by State Matrix for a gen_tibble object

Description

This function computes the IBS matrix.

Usage

pairwise_ibs(
  x,
  as_matrix = FALSE,
  type = c("proportion", "adjusted_counts", "raw_counts"),
  block_size = bigstatsr::block_size(nrow(x))
)

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)

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.

Details

Note that monomorphic sites are currently considered. Remove monomorphic sites before running pairwise_king if this is a concern.

Examples

example_gt <- load_example_gt("gen_tbl")

pairwise_ibs(example_gt, type = "proportion")

# Alternatively, return a matrix
pairwise_ibs(example_gt, type = "proportion", as_matrix = TRUE)

# Adjust block_size
pairwise_ibs(example_gt, block_size = 2)

# Change type
pairwise_ibs(example_gt, type = "adjusted_counts")
pairwise_ibs(example_gt, type = "raw_counts")