Kinship coefficients
Compute the matrix of kinship coefficients (autosomal or X) of all members of
a pedigree. The founders may be inbred; see pedtools::founderInbreeding()
for how to set this up.
kinship(x, ids = NULL) kinshipX(x, ids = NULL)
x |
A pedigree, in the form of a |
ids |
Either a character of length 2, or NULL. In the former case, it
must contain the ID labels of two members of |
For two (not necessarily distinct) members A, B of a pedigree, their autosomal (resp. X) kinship coefficient is defined as the probability that random alleles sampled from A and B at the same autosomal (resp. X) locus, are identical by descent relative to the pedigree.
If ids = NULL, a symmetric matrix containing all pairwise kinship coefficients in
x.
If ids has length 2, the function returns a single number.
# Kinship coefficients in a nuclear family with two children x = nuclearPed(2) kinship(x) # X chromosomal kinship coefficients in the same family kinshipX(x) # Recalculate the autosomal kinships if the father is 100% inbred founderInbreeding(x, 1) = 1 kinship(x)
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