likPairs: 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

Usage

likPairs(a, b, cc, d, pa, pb, pc, pd, Delta, DeltaMatrix)

Arguments

a	Vector of positive integers (allele 1 of individual 1)
b	Vector of positive integers (allele 2 of individual 1)
cc	Vector of positive integers (allele 1 of individual 2)
d	Vector of positive integers (allele 2 of individual 2)
pa	Double vector of allele frequencies
pb	Double vector of allele frequencies
pc	Double vector of allele frequencies
pd	Double vector of allele frequencies
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. See 'inbred::likPairsPed' for an implementation based 'ped-suite' input.

Value

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

See Also

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

Examples

library(pedtools)
library(ribd)
a  = c(1, 1, 1, 1)
b  = c(2, 2, 1, 2)
cc = c(1, 2, 2, 2)
d  = c(1, 2, 1, 1)
pa = p[a]
pb = p[b]
pc = p[cc]
pd = p[d]
H1 = halfSibPed(1)
p = c(0.4,  0.6)
# For plotting only
als = 1:length(p)
m = list()
for (i in 1:length(a))
   m[[i]] = marker(H1, afreq = p, alleles = als,
            "4" = c(a[i], b[i]), "5" = c(cc[i], d[i]) )
H1 = setMarkers(H1, m)
# plot(H1,m)

Delta1 = condensedIdentity(H1, c(4,5))
rho = 0.01
Delta2 = twoLocusIdentity(H1, c(4,5), rho)
lik1 = likPairs(a,b,cc,d, pa, pb, pc, pd, Delta = Delta1, DeltaMatrix = Delta2)
numerator = prod(lik1)
Delta1 = condensedIdentity(H1, c(1, 2))
rho = 0.5
Delta2 = matrix(0, ncol = 9, nrow = 9); Delta2[9,9] = 1
lik2 = likPairs(a,b,cc,d, pa, pb, pc, pd, Delta = Delta1, DeltaMatrix = Delta2)
denominator = prod(lik2)
numerator/denominator

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