R/getConc.R

In holgerschw/logicFS: Identification of SNP Interactions

getConc <- function (oob.eche, cl)
{
  y <- cl
  p <- ncol(y)
  time <- y[, p - 1]
  status <- y[, p]
  x <- oob.eche
  n <- length(time)
  ord <- order(time, -status)
  time <- time[ord]
  status <- status[ord]
  x <- x[ord]
  wh <- which(status == 1)
  total <- concordant <- 0
  for (i in wh){
    if (i < n){
      for (j in ((i + 1):n)){
        if (time[j] > time[i]){
          total <- total + 1
          if (x[j] < x[i]) 
            concordant <- concordant + 1
          if (x[j] == x[i]) 
            concordant <- concordant + 0.5
        } else if (status[j] == 1){
          total <- total + 1
          if (x[j] == x[i]){
            concordant <- concordant + 1
          } else concordant <- concordant + 0.5
        } else {
          total <- total + 1
          if (x[j] < x[i]){
            concordant <- concordant + 1
          } else concordant <- concordant + 0.5
        }
      }
    }
  }
  concordant / total
}