tools/simulators/popudepth/maf.r

   1 # generate genotype for each individual
   2 genotype=function(nsample,MAF) { # nsample为多少个个体，MAF为一维数组，存储所有SNP位点的MAF值
   3         nsite=length(MAF)
   4         a=array(runif(nsite*nsample*2,0,1),dim=c(nsite,2*nsample))
   5         b=a
   6         # generate genotype for each allele
   7         for (i in 1:nsite){
   8                 for (j in 1:(2*nsample)){
   9                         if (a[i,j]>MAF[i]) { b[i,j] = 0 }
  10                          else { b[i,j] = 1 }
  11                 }
  12         }
  13         # generate genotype for each individual: 00->0;11->3;01->1,10->2
  14         c=array(dim=c(nsite,nsample+2))
  15         for (i in 1:nsite){
  16                 c[i,1] = i # site ID
  17                 c[i,2] = MAF[i] # MAF value
  18                 for (j in seq(from=1,to=(2*nsample),by=2))
  19                  c[i,(j+1)/2+2]=b[i,j]*2+b[i,j+1]
  20         }
  21         return (c)
  22 }
  23
  24 genotype(5,c(0,.1,.2,.3,.4,.5,.6,.7,.8,.9,1))
  25 genotype(12,c(0,.05,.1,.2,.3,.4,.5))