tidypopgen (version 0.4.3)

pairwise_grm: Compute the Genomic Relationship Matrix for a gen_tibble object

Description

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 following the approach of Weir and Goudet 2017 based on beta estimators).

Usage

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

Value

a matrix of GR between all pairs of individuals

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 is 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.

Details

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

See Also

hierfstat::beta.dosage()

Examples

example_gt <- load_example_gt("gen_tbl")

# Compute the GRM from the allele sharing matrix
example_gt %>% pairwise_grm()

# To calculate using a precomputed allele sharing matrix, use:
allele_sharing <- example_gt %>% pairwise_allele_sharing(as_matrix = TRUE)
example_gt %>% pairwise_grm(allele_sharing_mat = allele_sharing)