likJStates: Likelihood for for all 9 Jacquard states

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

Description

Likelihood for for all 9 Jacquard states

Usage

likJStates(a, b, cc, d, pa, pb, pc, pd)

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

Value

A matrix with 9 rows and columns equal to the number of markers. Element (i,j) is the likelihood conditioned on Jacquard state i for marker j.

Examples

p = c(0.1, 0.2, 0.3, 0.4)
a  = c(1,1)
b  = c(2,2)
cc = c(3,1)
d  = c(4,2)
pa = p[a]
pb = p[b]
pc = p[cc]
pd = p[d]
Delta = c(0, 0, 0, 0, 0, 0, 1,0, 0) #unrelated
l2 = likJStates(a,b,cc,d, pa,pb,pc,pd)

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