tidypopgen (version 0.4.3)

snp_king: 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
)

Value

a square symmetrical matrix of relationship coefficients between individuals

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.

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)