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
genotypesslot 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.
Examples
example_gt <- load_example_gt("gen_tbl")
X <- attr(example_gt$genotypes, "bigsnp")
snp_king(X$genotypes)
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,] 0.500 0.00 0.125 0.250 0.250 -0.50 0.250
#> [2,] 0.000 0.50 NaN 0.000 -1.250 -1.00 -1.000
#> [3,] 0.125 NaN 0.500 0.000 0.125 -0.50 -0.750
#> [4,] 0.250 0.00 0.000 0.500 -0.625 -0.25 -0.125
#> [5,] 0.250 -1.25 0.125 -0.625 0.500 -1.00 -0.125
#> [6,] -0.500 -1.00 -0.500 -0.250 -1.000 0.50 NaN
#> [7,] 0.250 -1.00 -0.750 -0.125 -0.125 NaN 0.500
# Compute for individuals 1 to 5
snp_king(X$genotypes, ind.row = 1:5, ind.col = 1:5)
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0.50 0.0 0.00 0.25 0.25
#> [2,] 0.00 0.5 NaN 0.00 -1.00
#> [3,] 0.00 NaN 0.50 -0.25 -0.25
#> [4,] 0.25 0.0 -0.25 0.50 -0.50
#> [5,] 0.25 -1.0 -0.25 -0.50 0.50
# Adjust block size
snp_king(X$genotypes, block.size = 2)
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,] 0.500 0.00 0.125 0.250 0.250 -0.50 0.250
#> [2,] 0.000 0.50 NaN 0.000 -1.250 -1.00 -1.000
#> [3,] 0.125 NaN 0.500 0.000 0.125 -0.50 -0.750
#> [4,] 0.250 0.00 0.000 0.500 -0.625 -0.25 -0.125
#> [5,] 0.250 -1.25 0.125 -0.625 0.500 -1.00 -0.125
#> [6,] -0.500 -1.00 -0.500 -0.250 -1.000 0.50 NaN
#> [7,] 0.250 -1.00 -0.750 -0.125 -0.125 NaN 0.500