likPairsPed: Likelihood for two Possibly Inbred Individuals as a function...

In thoree/inbred: Different functions related to LR, bootstrap etc

Description

Likelihood for two Possibly Inbred Individuals as a function of the Condensed 'Jacquard' Coefficients with 'ped' input

Usage

likPairsPed(x, ids, Delta, DeltaMatrix)

Arguments

x	'ped' object with markers
ids	A vector oflength two identifying the individuals
Delta	Double vector of length 9 summing to unity
DeltaMatrix	Double 9x9 matrix of two locus identity coefficients

Details

The implementation is based on conditioning on IBD states at two linked loci. Currently, the recombination rate for each pair is assumed to be the same.

Value

The likelihood for the pairs. If there is an odd number of markers, the last marker is omitted for the elements of the list.

See Also

'ribd::condensedIdentity' and 'ribd::twoLocusIdentity'.'

Examples

x = pedtools::fullSibMating(1)
p = c(0.4, 0.6)
als = 1:length(p)
m1 = pedtools::marker(x, alleles = als, afreq = p, "5" = 1, "6" = 1)
m2 = pedtools::marker(x, alleles = als, afreq = p, "5" = 1:2, "6" = 1)
x = pedtools::setMarkers(x, list(m1, m2))
rho = 0.1
Delta1 = ribd::condensedIdentity(x, c(5, 6))
Delta2 = ribd::twoLocusIdentity(x, c(5, 6), rho)
ids = c(5,6)
l1 = likPairsPed(x, ids, Delta1, Delta2)
l2 = pedprobr::likelihood(x, m1, m2, rho)
abs(l1-l2) < 1e-10

thoree/inbred documentation built on March 28, 2021, 7:42 p.m.