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)
snp_allele_sharing(
X,
ind.row = bigstatsr::rows_along(X),
ind.col = bigstatsr::cols_along(X),
block.size = bigstatsr::block_size(nrow(X))
)
a bigstatsr::FBM.code256 matrix (as found in the genotypes
slot of a bigsnpr::bigSNP object).
An optional vector of the row indices that are used. If not specified, all rows are used. Don't use negative indices.
An optional vector of the column indices that are used. If not specified, all columns are used. Don't use negative indices.
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.
a matrix of allele sharing between all pairs of individuals