Inbreeding coefficients
Compute the inbreeding coefficients of all members of a pedigree. These are
simple wrappers of kinship() and kinshipX(). The founders may be inbred;
see pedtools::founderInbreeding() for how to set this up.
inbreeding(x, id = NULL) inbreedingX(x, id = NULL)
x |
A pedigree, in the form of a |
id |
Either a single ID label, or NULL (default). |
The autosomal inbreeding coefficient of a pedigree member is defined as the probability that, at a random autosomal locus, the two alleles carried by the member are identical by descent relative to the pedigree. It follows from the definition that the inbreeding coefficient of a member equals the kinship coefficient of the parents.
The X chromosomal inbreeding coefficient of an female member is defined similarly to the autosomal case above. For males is it always 1.
The inbreeding coefficients are computed from the diagonal of the kinship matrix, by the formula
f_a = 2*phi_aa - 1.
If id is NULL, the output is a named numeric vector of length
pedsize(x), containing the inbreeding coefficients of each pedigree
member. is returned.
If id is the label of a pedigree member, the inbreeding coefficient of
this individual is returned unnamed.
# Child of half siblings: f = 1/8 x = halfCousinPed(0, child = TRUE) inbreeding(x) # If the father is 100% inbred, the inbreeding coeff of the child doubles fa = commonAncestors(x, 4:5) # robust to label change founderInbreeding(x, fa) = 1 inbreeding(x) # Simpler output using the `id` argument: inbreeding(x, id = 6) ### X-chromosomal inbreeding coefficients ### # These depend on the genders in the pedigree. # To exemplify, we consider a child of half siblings. xPat = halfSibPed(sex2 = 2) # paternal half sibs xPat = addChildren(xPat, father = 4, mother = 5, nch = 1, sex = 2) stopifnot(inbreedingX(xPat, id = 6) == 0) # Change to maternal half sibs => coeff becomes 1/4. xMat = swapSex(xPat, 1) stopifnot(inbreedingX(xMat, id = 6) == 0.25) # Example with selfing and complete inbreeding s = selfingPed(1) founderInbreeding(s, 1) = 1 inbreeding(s, id = 2)
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