snp_king: Compute the KING-robust Matrix for a bigSNP object
In tidypopgen: Tidy Population Genetics

snp_king

R Documentation

Compute the KING-robust Matrix for a bigSNP object

Description

This function computes the KING-robust estimator of kinship.

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

Examples

example_gt <- load_example_gt("gen_tbl")

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

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

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

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.