R/GSEA.NormalizeCols.R

In GSEA-MSigDB/GSEA_R: Gene Set Enrichment Analysis (GSEA)

#' Standardize columns of a gene expression matrix
#'
#' `GSEA.NormalizeCols` performs column-wise normalization of a gene expression matrix using the col.mean and standard deviation
#'
#' Internal `GSEA` function.
#'
#' @keywords internal
#'

GSEA.NormalizeCols <-
function(V) {

 col.mean <- apply(V, MARGIN = 2, FUN = mean)
 col.sd <- apply(V, MARGIN = 2, FUN = sd)
 col.n <- length(V[1, ])
 for (i in 1:col.n) {
  if (col.sd[i] == 0) {
   V[, i] <- 0
  } else {
   V[, i] <- (V[, i] - col.mean[i])/col.sd[i]
  }
 }
 return(V)
}