R/pp_exp.R

In imsig: Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours

#' @title Pre-processing expression matrix
#' @description Subsets the user's dataset based on the genes that are common to the users dataset and ImSig.
#' @param exp Dataframe of transcriptomic data (natural scale) containing genes as rows and samples as columns. Note: Gene names should be set as row names and duplicates are not allowed. Missing values are not allowed within the expression matrix. Check example- head(example_data): \code{\link{example_data}}.
#' @return Expression dataframe

pp_exp <- function(exp){
  sig <- sig
  #g <- Reduce(intersect, list(as.character(row.names(exp), sig$gene)))
  g <- intersect(row.names(exp), as.character(sig$gene))
  exp <- exp [as.character(g),]
  return(exp)
}