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Compute the Pairwise Allele Sharing Matrix for a bigSNP object

Source: R/snp_allele_sharing.R
snp_allele_sharing.Rd

This function computes the Allele Sharing matrix. Estimates Allele Sharing (matching in hierfstat)) between pairs of individuals (for each locus, gives 1 if the two individuals are homozygous for the same allele, 0 if they are homozygous for a different allele, and 1/2 if at least one individual is heterozygous. Matching is the average of these 0, 1/2 and 1s)

Usage

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

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. Note that, to optimise the speed of matrix operations, we have to store in memory 3 times the columns.

Value

a matrix of allele sharing between all pairs of individuals

Examples

example_gt <- load_example_gt("gen_tbl")

X <- attr(example_gt$genotypes, "bigsnp")
snp_allele_sharing(X$genotypes)
#>           [,1]  [,2]  [,3]      [,4]      [,5]  [,6]  [,7]
#> [1,] 0.6666667 0.700 0.600 0.6666667 0.5833333 0.600 0.500
#> [2,] 0.7000000 0.900 0.750 0.8000000 0.5000000 0.500 0.375
#> [3,] 0.6000000 0.750 0.800 0.6000000 0.6000000 0.625 0.500
#> [4,] 0.6666667 0.800 0.600 0.8333333 0.4166667 0.700 0.500
#> [5,] 0.5833333 0.500 0.600 0.4166667 0.7500000 0.500 0.500
#> [6,] 0.6000000 0.500 0.625 0.7000000 0.5000000 0.900 0.750
#> [7,] 0.5000000 0.375 0.500 0.5000000 0.5000000 0.750 0.700

# Compute for individuals 1 to 5
snp_allele_sharing(X$genotypes, ind.row = 1:5, ind.col = 1:5)
#>       [,1]      [,2]      [,3]  [,4]  [,5]
#> [1,] 0.600 0.6250000 0.6250000 0.600 0.600
#> [2,] 0.625 0.8750000 0.8333333 0.750 0.500
#> [3,] 0.625 0.8333333 0.8750000 0.625 0.625
#> [4,] 0.600 0.7500000 0.6250000 0.800 0.400
#> [5,] 0.600 0.5000000 0.6250000 0.400 0.800

# Adjust block size
snp_allele_sharing(X$genotypes, block.size = 2)
#>           [,1]  [,2]  [,3]      [,4]      [,5]  [,6]  [,7]
#> [1,] 0.6666667 0.700 0.600 0.6666667 0.5833333 0.600 0.500
#> [2,] 0.7000000 0.900 0.750 0.8000000 0.5000000 0.500 0.375
#> [3,] 0.6000000 0.750 0.800 0.6000000 0.6000000 0.625 0.500
#> [4,] 0.6666667 0.800 0.600 0.8333333 0.4166667 0.700 0.500
#> [5,] 0.5833333 0.500 0.600 0.4166667 0.7500000 0.500 0.500
#> [6,] 0.6000000 0.500 0.625 0.7000000 0.5000000 0.900 0.750
#> [7,] 0.5000000 0.375 0.500 0.5000000 0.5000000 0.750 0.700