R/enrichRSCE.R

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

#' enrichR
#' Given a list of genes this function runs the enrichR() to perform Gene
#' enrichment
#'
#' @param inSCE Input \linkS4class{SingleCellExperiment} object.
#' @param glist selected genes for enrichment analysis using enrichR(). Required
#' @param db selected database name from the enrichR database list. if NULL then
#' enrichR will be run on all the available databases on the enrichR database.
#'
#' @return enrichRSCE(): returns a data.frame of enrichment terms overlapping in
#' the respective databases along with p-values, z-scores etc.,
#' @export
#' @examples
#' \dontrun{
#' enrichRSCE(mouseBrainSubsetSCE, "Cmtm5", "GO_Cellular_Component_2017")
#' }
enrichRSCE <- function(inSCE, glist, db = NULL){
  internetConnection <- suppressWarnings(Biobase::testBioCConnection())
  #check for internet connection
  if (!internetConnection){
    stop("Please connect to the Internet and continue..")
  }

  enrdb <- enrichR::listEnrichrDbs()$libraryName

  if (!inherits(inSCE, "SingleCellExperiment")){
    stop("Please use a SingleCellExperiment object")
  }

  #test for gene list existing
  if (!all(glist %in% rownames(inSCE))){
    stop("Gene in gene list not found in input object.")
  }

  #test for db existing
  if (!all(db %in% enrdb)){
    stop("database '", db, "' does not exist.")
  }

  if (is.null(glist)){
    stop("Please provide a gene list.")
  } else {
    if (is.null(db)){
      db <- enrdb
    }
    enriched <- enrichR::enrichr(glist, db)
    enriched <- data.frame(data.table::rbindlist(enriched, use.names = TRUE,
                                                 fill = TRUE,
                                                 idcol = "Database_selected"))
    temp_db <- enrichR::listEnrichrDbs()
    enriched$link <- vapply(enriched$Database_selected, function(x){
      temp_db$link[which(temp_db$libraryName %in% x)]
    }, FUN.VALUE = character(1))

    #sort the results based on p-values
    enriched <- enriched[base::order(enriched$P.value, decreasing = FALSE), ]

    #round the numeric values to their 7th digit
    nums <- vapply(enriched, is.numeric, FUN.VALUE = logical(1))
      enriched[, nums] <- base::round(enriched[, nums], digits = 7)
  }
  return(enriched)
}