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Compute the Genomic Relationship Matrix for a gen_tibble object

pairwise_grm.Rd

This function computes the Genomic Relationship Matrix (GRM). This is estimated by computing the pairwise kinship coefficients (coancestries) between all pairs of individuals from a matrix of Allele Sharing follwng the approach of Weir and Goudet 2017 based on beta estimators).

Usage

pairwise_grm(
  x,
  allele_sharing_mat = NULL,
  block_size = bigstatsr::block_size(count_loci(x))
)

Arguments

x

a gen_tibble object.

allele_sharing_mat

optional, the matrix of Allele Sharing returned by pairwise_allele_sharing() with as_matrix=TRUE. As a number of statistics can be derived from the Allele Sharing matrix, it it sometimes more efficient to pre-compute this matrix.

block_size

the size of the blocks to use for the computation of the allele sharing matrix.

Value

a matrix of GR between all pairs of individuals

Details

The GRM is twice the coancestry matrix (e.g. as estimated by hierfstat::beta.dosage() with inb=FALSE).