getASubset: Subset of additive relationship matrix

In Rpedigree/pedigreeTools: Versatile Functions for Working with Pedigrees

Subset of additive relationship matrix

Description

Returns subset of the additive relationship matrix for the pedigree.

Usage

getASubset(ped, labs)

Arguments

ped	pedigree
labs	a character vector or a factor giving individual labels to which to restrict the relationship matrix and corresponding factor using Colleau et al. (2002) algorithm. If labs is a factor then the levels of the factor are used as the labels. Default is the complete set of individuals in the pedigree.

Value

matrix (dsCMatrix - symmetric sparse)

References

Colleau, J.-J. An indirect approach to the extensive calculation of relationship coefficients. Genet Sel Evol 34, 409 (2002). https://doi.org/10.1186/1297-9686-34-4-409

Examples

ped <- pedigree(sire = c(NA, NA, 1,  1, 4, 5),
                dam =  c(NA, NA, 2, NA, 3, 2),
                label = 1:6)
(A <- getA(ped))
(ASubset  <- A[4:6, 4:6])
(ASubset2 <- getASubset(ped, labs = 4:6))

(ASubset3  <- A[6:4, 6:4])
(ASubset4 <- getASubset(ped, labs = 6:4))

# Test for correctness
stopifnot(!any(abs(ASubset - ASubset2) > .Machine$double.eps))
stopifnot(!any(abs(ASubset3 - ASubset4) > .Machine$double.eps))
stopifnot(Matrix::isSymmetric(ASubset2))
stopifnot(Matrix::isSymmetric(ASubset4))

Rpedigree/pedigreeTools documentation built on Oct. 13, 2023, 9:49 p.m.