case: Case determination for a pair of individuals

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

Description

This is a reduced version of the function 'likJ'. It only returns the 'casew' variable oflikJ

Usage

case(a, b, cc, d)

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)

Value

'case'

Examples

# Below I go through some cases trying to figure out
# what the LD probabilities should be

p = c(1,2,3,4,5)/sum(1:5)
H = p%o%p # Haplotypeprobs for LE

### Case  1,1
a  = c(1, 2)
b  = c(1, 2)
cc = c(1, 2)
d  = c(1, 2)
(Case = case(a,b,cc,d))
pa = p[a]
pb = p[b]
pc = p[cc]
pd = p[d]
Delta = c(1, 0, 0, 0, 0, 0, 0, 0, 0)
lik.LE = prod(likJ(a, b, cc, d, pa, pb, pc, pd, Delta))
lik.LD = H[a[1], a[2]]
lik.LD = geno1(cc[1], d[1], cc[2], d[2], H)
abs(lik.LE -lik.LD) < 1e-15

### Case 1,2
a  = c(1, 1)
b  = c(1, 1)
cc = c(1, 2)
d  = c(1, 2)
(Case = case(a,b,cc,d))
pa = p[a]
pb = p[b]
pc = p[cc]
pd = p[d]
Delta1 = c(1, 0, 0, 0, 0, 0, 0, 0, 0)
Delta2 = c(0, 1, 0, 0, 0, 0, 0, 0, 0)
lik.LE = likJ(a[1], b[1], cc[1], d[1], pa[1], pb[1], pc[1], pd[1], Delta1)*
         likJ(a[2], b[2], cc[2], d[2], pa[2], pb[2], pc[2], pd[2], Delta2)
# P(G1,G2|Jst)= P(G1|Jst, G2)  * P(G2|Jst) = p[a[[1]]]*H[cc[1],cc[2]]
lik.LD = p[a[[2]]]*H[cc[1],cc[2]]
lik.LD = p[a[[2]]]*geno1(cc[1], d[1], cc[2], d[2], H)
abs(lik.LE -lik.LD) < 1e-15

### Case 2,1
a  = c(1, 1)
b  = c(1, 1)
cc = c(2, 1)
d  = c(2, 1)
(Case = case(a,b,cc,d))
pa = p[a]
pb = p[b]
pc = p[cc]
pd = p[d]
Delta1 = c(0, 1, 0, 0, 0, 0, 0, 0, 0)
Delta2 = c(1, 0, 0, 0, 0, 0, 0, 0, 0)
lik.LE = likJ(a[1], b[1], cc[1], d[1], pa[1], pb[1], pc[1], pd[1], Delta1)*
         likJ(a[2], b[2], cc[2], d[2], pa[2], pb[2], pc[2], pd[2], Delta2)
# P(G1,G2|Jst)= P(G1|Jst, G2)  * P(G2|Jst) = p[a[[1]]]*H[cc[1],cc[2]]
lik.LD = p[a[[1]]]*H[cc[1],cc[2]]
lik.LD = p[a[[1]]]*geno1(cc[1], d[1], cc[2], d[2], H)
abs(lik.LE -lik.LD) < 1e-15

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