IBDsim (version 0.9-8)

oneLocusIBD: Estimating pairwise IBD coefficients

Description

Estimates by simulation the IBD coefficients of a non-inbred pairwise relationship.

Usage

oneLocusIBD(x, ind1, ind2, Nsim, Xchrom=FALSE, verbose=TRUE, ...)

Arguments

x

A pedigree in the form of a linkdat object.

ind1, ind2

Numeric ID labels of the two individuals.

Nsim

The number of simulations to be performed.

Xchrom

A logical indicating if the locus is X-linked (if TRUE) or autosomal (FALSE).

verbose

A logical.

…

Further arguments to be passed on to IBDsim.

Value

A numeric of length 3 (autosomal) or 2 (X-linked), estimating \(\kappa\).

Details

For any pair of non-inbred individuals, the IBD coefficients \(\kappa=(\kappa[0], \kappa[1], \kappa[2])\) associated with the relationship, are defined as the probabilities $$\kappa[i] = Pr(i alleles shared identically by descent).$$

For an X-chromosomal locus, and if at least one of the individuals is male, \(\kappa[i]\) is defined only for \(i=0,1\).

See Also

twoLocusIBD, oneLocusJacquard, twoLocusJacquard

Examples

# NOT RUN {
### Example 1: Full siblings
x <- nuclearPed(2) 
Nsim <- 100 # Should be increased substantially

# Autosomal kappa estimate (exact = c(0.25, 0.5, 0.25))
oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim)

# X-chromosomal kappa estimate (exact = c(0.5, 0.5))
oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, Xchrom=TRUE)

# }