R/load.TargetFile.R

In sarangian/RNASeqDEA: Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

#' Load target file
#'
#' Load the target file containing sample information
#'
#' @param targetFile path to the target file
#' @param varInt variable on which sorting the target
#' @param condRef reference condition of \code{varInt}
#' @param batch batch effect to take into account
#' @return A \code{data.frame} containing the informations about the samples (name, file containing the counts and biological condition)
#' @details The \code{batch} parameter is used only to check if it is available in the target file before running the suite of the script.
#' @author Marie-Agnes Dillies and Hugo Varet

loadTargetFile <- function(targetFile, varInt, condRef, batch){
  target <- read.table(targetFile, header=TRUE, sep="\t", na.strings="")
  if (!I(varInt %in% names(target))) stop(paste("The factor of interest", varInt, "is not in the target file"))
  if (!is.null(batch) && !I(batch %in% names(target))) stop(paste("The batch effect", batch, "is not in the target file")) 
  target[,varInt] <- as.factor(target[,varInt])
  if (!I(condRef %in% as.character(target[,varInt]))) stop(paste("The reference level", condRef, "is not a level of the factor of interest"))
  target[,varInt] <- relevel(target[,varInt],ref=condRef)
  target <- target[order(target[,varInt]),]
  rownames(target) <- as.character(target[,1])
  # check if varInt contains replicates
  if (min(table(target[,varInt]))<2) stop(paste("The factor of interest", varInt, "has a level without replicates"))
  # check if NA in the target
  if (any(is.na(cbind(target[,c(varInt, batch)], target[,1:2])))) stop("NA are present in the target file")
  # warning message if batch is numeric
  if (!is.null(batch) && is.numeric(target[,batch])) warning(paste("The", batch, "variable is numeric. Use factor() or rename the levels with letters to convert it into a factor"))
  if (any(grepl("[[:punct:]]", as.character(target[,varInt])))) stop(paste("The", varInt, "variable contains punctuation characters, please remove them"))
  cat("Target file:\n")
  print(target)
  return(target)
}