Query Relationship Coefficients from a Pedigree Matrix

Retrieves relationship coefficients between individuals from a pedmatrix object. For compact matrices, automatically handles lookup of merged full-siblings.

Usage

query_relationship(x, id1, id2 = NULL)

Arguments

x

A pedmatrix object created by pedmatrix.

id1

Character, first individual ID.

id2

Character, second individual ID. If NULL, returns the entire row of relationships for id1.

Value

• If id2 is provided: numeric value (relationship coefficient)

• If id2 is NULL: named numeric vector (id1's row)

• Returns NA if individual not found

Details

For compact matrices (compact = TRUE), this function automatically maps individuals to their family representatives. For methods A, D, and AA, it can compute the correct relationship even between merged full-siblings using the formula:

• A: \(a_{ij} = 0.5 * (a_{is} + a_{id})\) where s, d are parents

• D: \(d_{ij} = a_{ij}^2\) (for full-sibs in same family)

• AA: \(aa_{ij} = a_{ij}^2\)

Note

Inverse matrices (Ainv, Dinv, AAinv) are not supported because inverse matrix elements do not represent meaningful relationship coefficients.

See also

pedmatrix, expand_pedmatrix

Examples

tped <- tidyped(small_ped)
A <- pedmatrix(tped, method = "A", compact = TRUE)

# Query specific pair
query_relationship(A, "A", "B")
#> [1] 0

# Query merged full-siblings (works with compact)
query_relationship(A, "Z1", "Z2")
#> [1] 0.5507812

# Get all relationships for one individual
query_relationship(A, "A")
#>       A       B       F       I      J1      J2       N       O       R       C 
#> 1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.50000 
#>       E       Q       G       H       K       M       T       U       V       W 
#> 0.50000 0.00000 0.25000 0.25000 0.25000 0.25000 0.00000 0.12500 0.25000 0.12500 
#>       X       Y      Z1 
#> 0.18750 0.06250 0.09375