R/merge_windows.R

In rr1859/R.4Cker: Analysis of 4C-seq (circularized chromosome conformation capture) data

#merge windows
merge_windows = function(windows){
  output = NULL
  chr=as.character(windows[1,1])
  start=windows[1,2]
  end=windows[1,3]
  if(nrow(windows) > 2){
    for(i in 2:nrow(windows)){
      if(as.character(windows[i,1]) == chr & windows[i,2] <= end & windows[i,2] >= start){
        end=windows[i,3]
      }
      else{
        output=rbind(output, c(chr,start, end))
        chr=as.character(windows[i,1])
        start=windows[i,2]
        end=windows[i,3]
      }
    }
    return(data.frame(output))
  } else{
    return(windows)
  }
}