constructPedigree: Pedigree construction

In magnusdv/ribd: Pedigree-based Relatedness Coefficients

Pedigree construction

Description

Construct a pedigree yielding a prescribed set of IBD coefficients.

Usage

constructPedigree(kappa, describe = TRUE, verbose = FALSE)

Arguments

kappa	A probability vector of length 3; (kappa0, kappa1, kappa2).
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.

Details

The construction follows the method and formulae given in Vigeland (2020).

Value

A ped object containing a pair of double half cousins with inbred founders. (In corner cases the relationship collapses into siblings.)

References

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")}

Examples

# 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)

magnusdv/ribd documentation built on March 29, 2024, 5:20 a.m.