Nothing
internal_loop <- function(ctFile){
RNAstructure <- matrix(c(as.numeric(ctFile[,5]),as.numeric(ctFile[,6])),ncol = 2,byrow = F)
internal_loops <- list()
n <- 1
boundStart <- 0
boundEnd <- 0
boundStart2 <- 0
boundEnd2 <- 0
loops <- c()
for (i in 1:(dim(RNAstructure)[1] - 1)) {
if(RNAstructure[i,1] != 0 && RNAstructure[i+1,1] == 0){
boundStart <- i
}
if(RNAstructure[i,1] == 0 && RNAstructure[i+1,1] != 0){
boundEnd <- i + 1
}
if(boundStart == 0 && boundEnd != 0){
boundEnd <- 0
}
if(boundStart != 0 && boundEnd !=0){
#print(paste(boundStart,"_",boundEnd))
boundStart2 <- RNAstructure[boundStart,1]
boundEnd2 <- RNAstructure[boundEnd,1]
num_min <- min(boundStart2,boundEnd2) + 1
num_max <- max(boundStart2,boundEnd2) - 1
loop <- RNAstructure[num_min:num_max,1]
if(length(which(loop != 0)) == 0 && (boundStart + 1) != num_min && (boundEnd - 1) != num_max){
if(length(which(loops == (min(boundStart,boundEnd) + 1))) == 0){
loops <- c(loops,boundStart,boundEnd,num_min,num_max)
internal_loops[[n]] <- sort(c(num_min:num_max,(min(boundStart,boundEnd)+1):(max(boundStart,boundEnd)-1)))
n <- n + 1
}
}
boundStart <- 0
boundEnd <- 0
boundStart2 <- 0
boundEnd2 <- 0
}
}
return(internal_loops)
}
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