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Compute the Genomic Relationship Matrix for a gen_tibble object

Source: R/pairwise_grm.R
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 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))
)

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).

Examples

example_gt <- example_gt("gen_tbl")

# Compute the GRM from the allele sharing matrix
example_gt %>% pairwise_grm()
#>              a          b           c           d            e           f
#> a  0.396946565  0.5572519  0.07633588  0.39694656 -0.003816794  0.07633588
#> b  0.557251908  1.5190840  0.79770992  1.03816794 -0.404580153 -0.40458015
#> c  0.076335878  0.7977099  1.03816794  0.07633588  0.076335878  0.19656489
#> d  0.396946565  1.0381679  0.07633588  1.19847328 -0.805343511  0.55725191
#> e -0.003816794 -0.4045802  0.07633588 -0.80534351  0.797709924 -0.40458015
#> f  0.076335878 -0.4045802  0.19656489  0.55725191 -0.404580153  1.51908397
#> g -0.404580153 -1.0057252 -0.40458015 -0.40458015 -0.404580153  0.79770992
#>            g
#> a -0.4045802
#> b -1.0057252
#> c -0.4045802
#> d -0.4045802
#> e -0.4045802
#> f  0.7977099
#> g  0.5572519

# 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)
#>              a          b           c           d            e           f
#> a  0.396946565  0.5572519  0.07633588  0.39694656 -0.003816794  0.07633588
#> b  0.557251908  1.5190840  0.79770992  1.03816794 -0.404580153 -0.40458015
#> c  0.076335878  0.7977099  1.03816794  0.07633588  0.076335878  0.19656489
#> d  0.396946565  1.0381679  0.07633588  1.19847328 -0.805343511  0.55725191
#> e -0.003816794 -0.4045802  0.07633588 -0.80534351  0.797709924 -0.40458015
#> f  0.076335878 -0.4045802  0.19656489  0.55725191 -0.404580153  1.51908397
#> g -0.404580153 -1.0057252 -0.40458015 -0.40458015 -0.404580153  0.79770992
#>            g
#> a -0.4045802
#> b -1.0057252
#> c -0.4045802
#> d -0.4045802
#> e -0.4045802
#> f  0.7977099
#> g  0.5572519