R/ratiog.R

In bapred: Batch Effect Removal and Addon Normalization (in Phenotype Prediction using Gene Data)

ratiog <-
function(x, batch) {

  if(any(is.na(x)))
	stop("Data contains missing values.")
  if(!is.factor(batch))
    stop("'batch' has to be of class 'factor'.")  
  if(!is.matrix(x))
    stop("'x' has to be of class 'matrix'.") 

  batches = levels(batch)
  nbatches = length(batches)

  means = as.list(rep(0,nbatches))
  xadj = x  
  for (i in 1:nbatches) {
    xadj[batch==batches[i],] <- apply(x[batch==batches[i],], 2, function(x) {
	  if(all(x <= 0))
	    x <- rep(min(-(x[x < 0])), length(x))
	  else
    	x[x<=0] <- min(x[x>0])
	  x
	})
    means[[i]] <- apply(xadj[batch==batches[i],], 2, function(x) exp(mean(log(x))))
    xadj[batch==batches[i],] = scale(xadj[batch==batches[i],],center=rep(0,ncol(xadj)),scale=means[[i]])
  }
  
  params <- list(xadj=xadj)
  params$nbatches <- nbatches
  params$batch <- batch  
  
  class(params) <- "ratiog"
   
  return(params)

}