snp_ibs.Rd
This function computes the IBS matrix.
snp_ibs(
X,
ind.row = bigstatsr::rows_along(X),
ind.col = bigstatsr::cols_along(X),
type = c("proportion", "adjusted_counts", "raw_counts"),
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.
one of "proportion" (equivalent to "ibs" in PLINK), "adjusted_counts" ("distance" in PLINK), and "raw_counts" (the counts of identical alleles and non-missing alleles, from which the two other quantities are computed)
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.
if as.counts = TRUE function returns a list of two bigstatsr::FBM matrices, one of counts of IBS by alleles (i.e. 2*n loci), and one of valid alleles (i.e. 2 * n_loci - 2 * missing_loci). If as.counts = FALSE returns a single matrix of IBS proportions.
Note that monomorphic sites are currently counted. Should we filter them beforehand? What does plink do?