snp_king: Compute the KING-robust Matrix for a bigSNP object

In tidypopgen: Tidy Population Genetics

Compute the KING-robust Matrix for a bigSNP object

Description

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

Usage

snp_king(
  X,
  ind.row = bigstatsr::rows_along(X),
  ind.col = bigstatsr::cols_along(X),
  block.size = bigstatsr::block_size(nrow(X)) * 4
)

Arguments

X	a bigstatsr::FBM.code256 matrix (as found in the genotypes slot of a bigsnpr::bigSNP object).
ind.row	An optional vector of the row indices that are used. If not specified, all rows are used. Don't use negative indices.
ind.col	An optional vector of the column indices that are used. If not specified, all columns are used. Don't use negative indices.
block.size	maximum number of columns read at once.

Value

a square symmetrical matrix of relationship coefficients between individuals

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.

Examples

example_gt <- load_example_gt("gen_tbl")

X <- attr(example_gt$genotypes, "fbm")
snp_king(X)

# Compute for individuals 1 to 5
snp_king(X, ind.row = 1:5, ind.col = 1:5)

# Adjust block size
snp_king(X, block.size = 2)

tidypopgen documentation built on Jan. 23, 2026, 1:06 a.m.