tidypopgen (version 0.4.3)

pairwise_king: Compute the KING-robust Matrix for a gen_tibble object

Description

This function computes the KING-robust estimator of kinship, reimplementing the KING algorithm of Manichaikul et al. (2010).

Usage

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

Value

a square symmetrical matrix of relationship coefficients between individuals if as_matrix is TRUE, or a tidied tibble of coefficients if as_matrix is FALSE.

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.

References

Manichaikul, A. et al. (2010) Robust relationship inference in genome-wide association studies. Bioinformatics, 26(22), 2867–2873. https://doi.org/10.1093/bioinformatics/btq559.

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")

# Compute the KING-robust matrix
pairwise_king(example_gt, as_matrix = TRUE)

# Or return a tidy tibble
pairwise_king(example_gt, as_matrix = FALSE)

# Adjust block_size
pairwise_king(example_gt, block_size = 2)