Compute the Pairwise Allele Sharing Matrix for a bigSNP object
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.