pedigreeTools (version 0.2)

relfactor: Relationship factor from a pedigree

Description

Determine the right Cholesky factor of the relationship matrix for the pedigree ped, possibly restricted to the specific labels that occur in labs.

Usage

relfactor(ped, labs = NULL)
getL(ped, labs = NULL)

Value

matrix (dtCMatrix - upper triangular sparse)

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.

Functions

• getL(): Relationship factor from a pedigree

Details

Note that the right Cholesky factor is returned, which is upper triangular, that is from A = LL' = R'R (lower (upper triangular) and not L (lower triangular) as the function name might suggest.

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)
(L <- getL(ped))
chol(getA(ped))

# Test for correctness
LExp <- matrix(data = c(1.0000, 0.0000, 0.5000, 0.5000, 0.5000, 0.2500,
                        0.0000, 1.0000, 0.5000, 0.0000, 0.2500, 0.6250,
                        0.0000, 0.0000, 0.7071, 0.0000, 0.3536, 0.1768,
                        0.0000, 0.0000, 0.0000, 0.8660, 0.4330, 0.2165,
                        0.0000, 0.0000, 0.0000, 0.0000, 0.7071, 0.3536,
                        0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.6847),
               byrow = TRUE, nrow = 6)
stopifnot(!any(abs(round(L, digits = 4) - LExp) > .Machine$double.eps))
LExp <- chol(getA(ped))
stopifnot(!any(abs(L - LExp) > .Machine$double.eps))

(L <- getL(ped, labs = 4:6))
(LExp <- chol(getA(ped)[4:6, 4:6]))
stopifnot(!any(abs(L - LExp) > .Machine$double.eps))