twoLocusInbreeding {ribd}

Two-locus inbreeding

Description

Computes the two-locus inbreeding coefficient of a pedigree member, for a given recombination rate.

Usage

twoLocusInbreeding(x, id, rho, verbose = FALSE, debug = FALSE)

Arguments

x

A pedigree in the form of a pedtools::ped object.

id

The ID label of a pedigree member.

rho

A numeric vector of recombination rates; all entries must be in the interval [0, 0.5].

verbose

A logical.

debug

A logical. If TRUE, detailed messages are printed during the recursion process.

Details

Let A be a pedigree member, and L1, L2 two autosomal loci with recombination rate \rho. The two-locus inbreeding coefficient f_{11}(\rho) is defined as the probability that A is autozygous at both L1 and L2 simultaneously.

As in the one-locus case, the two-locus inbreeding coefficient of A equals the two-locus kinship coefficient of the parents.

References

Weir & Cockerham (1969). Pedigree mating with two linked loci. Genetics, 61:923-940.

See Also

twoLocusKinship(), twoLocusIBD(), twoLocusIdentity()

Examples

###################################################
# Reproducing an example of Weir & Cockerham (1969)
###################################################

# Pedigree
x = nuclearPed(2, sex = 1:2) |>
  addDaughter(3:4) |>
  addSon(c(3,5)) |>
  addDaughter(5:6) |>
  relabel(new = strsplit("GHDECBA","")[[1]])

plot(x)

# The two-locus inbreeding of A
twoLocusPlot(list(ped = x, ids = "A"), coeff = "inb")

# W&C formula (expressed by linkage parameter a = 1-2*rho)
rho = seq(0, 0.5, length = 11)
a = 1 - 2*rho
WC = (128 + 10*a + 36*a^2 + 47*a^3 + 20*a^4 + 10*a^5 + 4*a^6 + a^7)/512

points(rho, WC, col = 2)