R/hairpin_loop.R

In RNAsmc: RNA Secondary Structure Module Mining, Comparison and Plotting

hairpin_loop <- function(ctFile){
  RNAstructure <- matrix(c(as.numeric(ctFile[,5]),as.numeric(ctFile[,6])),ncol = 2,byrow = F)
  arr_line <- c()
  arr0 <- RNAstructure[,1]
  hairpin_loops <- list()
  n <- 1
  for(i in 1:dim(RNAstructure)[1]){
    num_min <- min(RNAstructure[i,1],RNAstructure[i,2])
    num_max <- max(RNAstructure[i,1],RNAstructure[i,2])
    arr <- arr0[(num_min+1):(num_max-1)]
    if(num_min != 0 && num_max != 0 && length(which(arr != 0)) == 0){
      line <- paste0(RNAstructure[i,1],"_",RNAstructure[i,2])
      line2 <- paste0(RNAstructure[i,2],"_",RNAstructure[i,1])
      arr_line <- c(arr_line,line)
      if(length(which(arr_line == line2))==0){
        hairpin_loops[[n]] <- (num_min+1):(num_max-1)
        n <- n + 1
      }
    }
  }
  if(length(hairpin_loops) == 0){
    hairpin_loops <- list()
    return(hairpin_loops)
  }else{
    hairpin_number <- length(hairpin_loops)
    hairpin_max <- length(hairpin_loops[[1]])
    hairpin_min <- length(hairpin_loops[[1]])
    for (i in 1:length(hairpin_loops)) {
      if(length(hairpin_loops[[i]]) > hairpin_max){
        hairpin_max <- length(hairpin_loops[[i]])
      }
      if(length(hairpin_loops[[i]]) < hairpin_min){
        hairpin_min <- length(hairpin_loops[[i]])
      }
    }
    hairpin_length <- length(unlist(hairpin_loops))
    hairpin_mean <- hairpin_length/hairpin_number
    attr(hairpin_loops,"number of bases in hairpin loops") <- hairpin_length
    attr(hairpin_loops,"number of hairpin loops") <- hairpin_number
    attr(hairpin_loops,"Maximum length of hairpin loops") <- hairpin_max
    attr(hairpin_loops,"Minimum length of hairpin loops") <- hairpin_min
    attr(hairpin_loops,"Average length of hairpin loops") <- hairpin_mean
    return(hairpin_loops)
  }
}