Calculate Partial Inbreeding

Decomposes individuals' inbreeding coefficients into marginal contributions from specific ancestors. This allows identifying which ancestors or lineages are responsible for the observed inbreeding.

Usage

pedpartial(ped, ancestors = NULL, top = 20)

Arguments

ped

A tidyped object.

ancestors

Character vector. IDs of ancestors to calculate partial inbreeding for. If NULL, the top ancestors by marginal contribution are used.

top

Integer. Number of top ancestors to include if ancestors is NULL.

Value

A data.table with the first column as Ind and subsequent columns representing the partial inbreeding ($pF$) from each ancestor.

Details

The sum of all partial inbreeding coefficients for an individual (including contributions from founders) equals $1 + f_i$, where $f_i$ is the total inbreeding coefficient. This function specifically isolates the terms in the Meuwissen & Luo (1992) decomposition that correspond to the selected ancestors.

References

Lacey, R. C. (1996). A formula for determining the partial inbreeding coefficient, \(F_{ij}\). Journal of Heredity, 87(4), 337-339.

Meuwissen, T. H., & Luo, Z. (1992). Computing inbreeding coefficients in large populations. Genetics Selection Evolution, 24(4), 305-313.

Examples

# \donttest{
library(data.table)
tp <- tidyped(inbred_ped)
# Calculate partial inbreeding originating from specific ancestors
target_ancestors <- inbred_ped[is.na(Sire) & is.na(Dam), Ind]
pF <- pedpartial(tp, ancestors = target_ancestors)
#> Calculating partial inbreeding for 2 ancestors...
print(tail(pF))
#>       Ind       A       B
#>    <char>   <num>   <num>
#> 1:      B 0.00000 0.00000
#> 2:      C 0.00000 0.00000
#> 3:      D 0.00000 0.00000
#> 4:      E 0.12500 0.12500
#> 5:      F 0.00000 0.25000
#> 6:      G 0.15625 0.28125
# }