oneLocusIBD {IBDsim}

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.

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.

Value

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

Author(s)

Magnus Dehli Vigeland

See Also

twoLocusIBD, oneLocusJacquard, twoLocusJacquard

Examples

### 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)