R/summary.R

In llrs/GSEAdv: Analyze Gene Sets Collections Properites

#' Calculates some statistics of the GeneSetCollection
#'
#' These statistics include the biggest pathway, the gene in more pathways,
#' h-index and entropy or information content for the genes per pathway and
#' pathways for genes and they percentage  of the maximum.
#' @param object A GeneSetCollection object
#' @return invisible a list of statistics
#' @author Lluís Revilla
#' @seealso \code{\link{genesPerPathway}}, \code{\link{pathwaysPerGene}}
#' @rdname summary
#' @aliases summary
#' @export
setMethod("summary",
          "GeneSetCollection",
          function(object) {
            object <- check(object)
            gpp <- genesPerPathway(object)
            ppg <- pathwaysPerGene(object)

            h_gpp <- h_index(gpp)
            h_ppg <- h_index(ppg)

            out <- c(ICgpp = IC(gpp),
                     ICppg = IC(ppg),
                     maxICgpp = maxIC(gpp),
                     maxICppg = maxIC(ppg),
                     genes = length(ppg),
                     maxGPP = max(gpp),
                     independence = independence(object),
                     isolation = isolation(object),
                     maxPPG = max(ppg),
                     pathways = length(gpp)
            )
            msg <- paste0("Genes: ", out["genes"],
                "\n\tGene in more pathways: ", out["maxPPG"], " pathways\n",
            "\th-index: ", h_gpp, " genes with at least ", h_gpp, " pathways.\n",
            "Pathways: ", out["pathways"], "\n",
            "\tBiggest pathway: ", out["maxGPP"], " genes\n",
            "\th-index: ", h_ppg, " pathways with at least ", h_ppg, " genes.\n")
            if (!out["independence"]) {
              ind <- paste0("IC(genesPerPathway): ", round(out["ICgpp"], 2),
                  " ( ", round(out["ICgpp"]/out["maxICgpp"], 2),
                  " of the maximum)\nIC(pathwaysPerGene): ",
                  round(out["ICppg"], 2), " ( ",
                  round(out["ICppg"]/out["maxICppg"], 2), " of the maximum)\n")
            } else {
              ind <- "All genes in a single gene set.\n"
            }
            if (out["isolation"]) {
              ind <- paste0(ind,
                            "Some gene set have all genes not present in other gene sets")
            }
            cat(paste0(msg, ind))
            invisible(out)
          }
)