R/combineDist.R

In arorarshi/MOSAIC:

###########################
# combineDist
###########################

combineDist<-function(dist.dat){
  arr <- array(unlist(dist.dat), dim = c(nrow(dist.dat[[1]]),ncol(dist.dat[[1]]),length(dist.dat)))
  #calculate mean distance after removing NA
  combMat <- rowMeans(arr, dim = 2, na.rm = TRUE)
  rownames(combMat) <- rownames(dist.dat[[1]])
  colnames(combMat) <- colnames(dist.dat[[1]])
  #copy the rest of the triangle
  combMat[lower.tri(combMat)] <- t(combMat)[lower.tri(combMat)]
  colna = colSums(is.na(combMat))
  tab.idx = sort(table(unlist(apply(combMat,2,function(x) which(is.na(x))))),decreasing=T)
  idx = as.numeric(names(tab.idx))
  iter=1
  combMatDel = combMat
  #remove incomplete pairwise information
  while(sum(is.na(combMatDel))!=0){
    if (iter==1){del.idx = idx[iter]}
    if (iter!=1){del.idx = c(del.idx, idx[iter])}
    combMatDel = combMat[-del.idx, -del.idx]
    iter = iter + 1
  }

  if(nrow(combMatDel) < 2){stop("only one sample left after overlaping for complete pairs, low sample overlap!")}
  return(combMatDel)
}