View source: R/constructPedigree.R
constructPedigree | R Documentation |
Construct a pedigree yielding a prescribed set of IBD coefficients.
constructPedigree(kappa, describe = TRUE, verbose = FALSE)
kappa |
A probability vector of length 3; |
describe |
A logical. If TRUE, a textual description of the resulting relationship is printed. |
verbose |
A logical. If TRUE, various details about the calculations are printed. |
The construction follows the method and formulae given in Vigeland (2020).
A ped
object containing a pair of double half cousins with inbred
founders. (In corner cases the relationship collapses into siblings.)
M. D. Vigeland (2020). Relatedness coefficients in pedigrees with inbred founders. Journal of mathematical biology. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1007/s00285-020-01505-x")}
# Full siblings
x = constructPedigree(kappa = c(0.25, 0.5, 0.25))
kappaIBD(x, leaves(x))
# A relationship halfway between parent-child and full sibs
kap = c(1/8, 6/8, 1/8)
showInTriangle(kap, label = " (1/8, 1/8)", pos = 4)
y = constructPedigree(kappa = kap)
plot(y)
stopifnot(all.equal(kappaIBD(y, leaves(y)), kap))
# kappa = (0,1,0) does not give a parent-child relationship,
# but half siblings whose shared parent is completely inbred.
z = constructPedigree(kappa = c(0,1,0))
plot(z)
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