R/prepMNT.R

In npham25/prepMNT: Preprocess the MNTs data

prepMNT <- function(x, seed=1234, pctZeroCut=75, freqCut = 19, uniqueCut = 20) 
 {
  #Transpose x
  
 #reproducable
  set.seed(seed)
  if (is.null(dim(x))) 
    x <- matrix(x, ncol = 1)
  
  x <- as.matrix(apply(x,2,function(x) as.numeric(as.character(x))))
  #the ratio of the most common value to the second most common value
  freqRatio <- apply(x, 2, function(data) {
    t <- table(data[!is.na(data)])
    if (length(t) <= 1) {
      return(0)
    }
    w <- which.max(t)
    return(max(t, na.rm = TRUE)/max(t[-w], na.rm = TRUE))
  })
  #	the percentage of distinct values out of the number of total samples
  lunique <- apply(x, 2, function(data) length(unique(data[!is.na(data)])))
  percentUnique <- 100 * lunique/apply(x, 2, length)
  #Percentage of zeros
  pctZero <- as.vector(apply(x, 2, function(x)  100*sum(x == 0, na.rm=T)/length(na.omit(x))))
  #Exclude MNTs which have 100% zeros or > 75%
  rmv <- pctZero == 100 | 
    (freqRatio > freqCut & percentUnique < uniqueCut & pctZero > pctZeroCut)
  #Remove lipids in x
  x <- x[, !rmv]
  #Replace 0 by ""
  x[x == 0] <- ""
  x <- as.matrix(apply(x,2,function(x) as.numeric(as.character(x))))
  return (QRILC_wrapper(x))
 }

QRILC_wrapper <- function(x, ...) 
{
  res <- imputeLCMD::impute.QRILC(log(x),...) 
  return(exp(res[[1]]))
}