AlleleFreqDyn.txt

# AlleleFreqDyn.txt - examines aspects of allele frequency changes under drift for
# purposes of devising tests of departure from neutrality based on observed allele 
# frequencies over generations.

# First show single generation allele frequency changes under binomial, 
# from random starts

N<-1000
nsamp<-10000
p<-runif(nsamp)
x<-rbinom(nsamp,N,p)
p1<-x/N
delta<-p1-p
plot(p,delta)

# Next use the same bit of code from the Wright-Fisher sim to generate allele 
# frequencies of replicate populations under the strict neutrality.

N<-200
nsamp<-8
ngen<-50
startfreq<-.5
pcur<-matrix(1:N)

#Wright-Fisher is simply recurrent binomial sampling over generations

x<-rbinom(nsamp,N,startfreq)
p<-x/N
pcur<-p

for (i in 1:ngen){
x<-rbinom(nsamp,N,p)
p<-x/N
pcur<-rbind(pcur,p)
}
gen<-seq(1,ngen)
for (k in 1:nsamp){
  plot(gen,pcur[,k],type="l",ylim=c(0,1))
  par(new=TRUE)
}



# ASSIGNMENT 1: For each of the sample data sets, try to devise a way to 
# estimate the population size N from the rate of increase in variance in 
# allele frequencies over generations.
# In the data sets, columns are distinct SNPs and rows are generations.



# ASSIGNMENT 2: It turns out that the sample data sets each have one SNP 
# that deviates from the neutral dynamics. Use whatever test you can 
# devise to determine which of the SNPs in the sample data sets appear to 
# depart from neutrality.