R/MIGSAres-getAdditionalInfo.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' Gets additional information about enrichment results
#'
#' \code{getAdditionalInfo} gets additional enrichment information of the
#' analysis done.
#'
#' @param migsaRes MIGSAres object.
#'
#' @return data.frame with additional information for each analyzed gene set.
#'
#' @docType methods
#' @name getAdditionalInfo
#' @rdname MIGSAres-getAdditionalInfo
#'
#' @exportMethod getAdditionalInfo
setGeneric(name = "getAdditionalInfo", def = function(migsaRes) {
  standardGeneric("getAdditionalInfo")
})

#' @rdname MIGSAres-getAdditionalInfo
#' @aliases getAdditionalInfo,MIGSAres
#' @include MIGSAres-class.R
#' @include MIGSAres-setEnrCutoff.R
#' @seealso \code{\link{setEnrCutoff}}
#' @examples
#' data(migsaRes)
#' ## Lets get additional enrichment information of the MIGSAres object.
#' adtnlInfo <- getAdditionalInfo(migsaRes)
#' dim(adtnlInfo)
#' # it is a huge data.frame
#'
#' ## This huge amount of information commonly is not that interesting. Lets
#' ## keep the gene sets that were enriched in every experiment and check that
#' ## information. Lets set a cutoff of 0.1.
#' migsaResWCoff <- setEnrCutoff(migsaRes, 0.1)
#' migsaResFiltered <- migsaResWCoff[rowSums(migsaResWCoff[, 4:5]) == 2, ]
#' adtnlInfo <- getAdditionalInfo(migsaResFiltered)
#' dim(adtnlInfo)
setMethod(
  f = "getAdditionalInfo",
  signature = c("MIGSAres"),
  definition = function(migsaRes) {
    res <- as.data.frame(migsaRes@migsa_res_all)
    return(res)
  }
)