# R/ldR.R In sdwfrost/popseq: Population Analysis of Deep Sequencing Data

#### Documented in ldR

```####a function to calculate the Linkage disequilibrium given two columns of 1s and 2s####
ld2=function(twocol){
require(plyr)
freq1=count(twocol[,1])
freq2=count(twocol[,2])
freq12=count(c(twocol[,1],twocol[,2]))
p1=freq1[2,2]/sum(freq1[,2])
p2=freq2[2,2]/sum(freq2[,2])
p12=freq12[2,2]/sum(freq12[,2])
num=p12-p1*p2
den=p1*p2*(1-p1-p2+p1*p2)
return(num^2/den)
}

####a function to calculate the Linkage disequilibrium of a sequences*SNPs matrix####
ldall=function(hapmatrix){
require(plyr)
hapmatrix=as.matrix(hapmatrix)
output=matrix(1,nrow=dim(hapmatrix)[2],ncol=dim(hapmatrix)[2])
for (i in 1:(dim(hapmatrix)[2]-1)){
for (j in (i+1):dim(hapmatrix)[2]){
output[i,j]=ld2(cbind(hapmatrix[,i],hapmatrix[,j]))
output[j,i]=output[i,j]
}
}
return(output)
}

#' A function to calculate Kelly's Zns statistic and the omega_max statistic given a haplotype matrix.
#'
#' @param hapmatrix A haplotype matrix with ones (ancestral) and twos (derived).
#' @return Kelly's Zns statistic, the omega_max statistic and the site produces omega_max.
#' @examples
#' exmtx=matrix(sample(2,80,replace=T),ncol=10,nrow=8)
#' ldR(exmtx)
#'
#' @author Fei Xiang (\email{[email protected]@gmail.com})
#'
#' @export
#'
ldR=function(hapmatrix){
require(plyr)
rmat=ldall(hapmatrix)
S=dim(hapmatrix)[2]
zns=(sum(rmat)-S)/S/(S-1)
omega=0
for (i in 1:(S-1)){
omega[i]=(sum(rmat[1:i,1:i])+sum(rmat[(i+1):S,(i+1):S])-S)/2/(choose(i,2)+choose(S-i,2))
omega[i]=omega[i]*i*(S-i)/(sum(rmat[1:i,(i+1):S]))
}

return(list(Zns=zns,omega_max=c(max(omega),which(omega==max(omega)))))
}
```
sdwfrost/popseq documentation built on Aug. 4, 2017, 7:21 p.m.