---
title: "ratio of homozygosity when inbred"
author: "Jérôme Goudet & Bruce Weir"
date: "15 juillet 2015"
output: html_document
---

On slide 196, the probability of being homozygote given $F$ is given as $P_{AA}=Fp_A+(1-F)p_A^2$.  Thus, an inbred individual with inbreeding coefficient $F$ is $Prob(AA|F)/Prob(AA|0)=F/p_A+(1-F)$  more likely to be homozygote than a non inbred individual.  Lets plot this:

```{r}
ratio.hom<-function(p,f) f/p+(1-f)
p<-seq(0.001,0.1,0.001)
plot(p,ratio.hom(p,f=0.125),type="l",log="x",ylab="Ratio Homozygosity",lwd=2)
abline(h=1,col="red")
```

Imagine we are looking at a rare recessive disease.  An inbred individual, when the allele frequency is low, is many times more likely to be affected than a non inbred individual.