R/loadExpr.R

In th86/gislkit: gislkit

#From Weiyi Cheng's Cafr
loadExpr <- function(file, sep='\t'){
  line <- readLines(file)
  tokens <- strsplit(line[1], "\t")[[1]]
  n <- length(tokens)-1
  m <- length(line)-1
  mset <- matrix(NA, m, n)	
  cname <- tokens[2:(n+1)]
  rname <- rep(NA, m)
  b <- txtProgressBar(style=3)
  for(i in 1:m){
    tokens <- strsplit(line[i+1], "\t")[[1]]
    tokens[tokens=="NA"] <- NA
    rname[i] <- tokens[1]
    mset[i,] <- as.numeric(tokens[2:(n+1)])
    if(i %% 100 == 0){
      setTxtProgressBar(b, i/m)
    }
  }
  cat("\n")
  colnames(mset) <- cname
  rownames(mset) <- rname
  mset
}