R/nDiffTotal.r

In sarangian/deaRscripts: 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

#' Number of differentially expressed features per comparison
#'
#' Number of down- and up-regulated features per comparison
#'
#' @param complete list of \code{data.frame} containing features results (from \code{exportResults.DESeq2()} or \code{exportResults.edgeR()})
#' @param alpha threshold to apply to the FDR
#' @return A matrix with the number of up, down and total of features per comparison
#' @author Marie-Agnes Dillies and Hugo Varet

nDiffTotal <- function(complete, alpha=0.05){
  nDiffTotal <- matrix(NA,ncol=4,nrow=length(complete),dimnames=list(names(complete),c("Test vs Ref", "# down","# up","# total")))
  for (name in names(complete)){
    complete.name <- complete[[name]]
    if (!is.null(complete.name$betaConv)){
	  nDiffTotal[name,2:3]=c(nrow(complete.name[which(complete.name$padj <= alpha & complete.name$betaConv & complete.name$log2FoldChange<=0),]),
                             nrow(complete.name[which(complete.name$padj <= alpha & complete.name$betaConv & complete.name$log2FoldChange>=0),]))
	} else{
	  nDiffTotal[name,2:3]=c(nrow(complete.name[which(complete.name$padj <= alpha & complete.name$log2FoldChange<=0),]),
                             nrow(complete.name[which(complete.name$padj <= alpha & complete.name$log2FoldChange>=0),]))	
	}
  }
  nDiffTotal[,4] <- nDiffTotal[,2] + nDiffTotal[,3]
  nDiffTotal[,1] <- gsub("_"," ",rownames(nDiffTotal))
  rownames(nDiffTotal) <- NULL
  return(nDiffTotal)
}