R/nwa_summarize.R

In CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

if (!isGeneric("summarize")) {
  setGeneric("summarize", function(object, what = "ALL", ...)
    standardGeneric("summarize"), package = "HTSanalyzeR2")
}

#' @include nwa_class.R
#' @describeIn summarize For an object of class NWA, the key words include 'Pval'
#' (the slot 'pvalues'), 'Phenotype' (the slot 'phenotypes'), 'Interactome' (the
#' slot 'interactome'), 'Para' (the slot 'fdr'), 'Result' (the slot 'result')
#' and 'ALL' (all slots).
#' @return In the end, this function would return a summary of the NWA object.
#' @examples
#' \dontrun{
#' # =================================================================
#' # NWA class
#' ## load a NWA object(see the examples of analyze NWA for details)
#' data(d7_nwa)
#'
#' ## summarize d7_nwa
#' summarize(d7_nwa, what = "ALL")
#' summarize(d7_nwa, what = "Result")
#' }
#' @export
setMethod("summarize", signature = "NWA",
          function(object, what = "ALL") {
            paraCheck("Summarize", "NWAwhat", what)
            if (any(c("ALL", "Pval") %in% what)) {
              cat("\n")
              cat("-p-values: \n")
              print(object@summary$input["p-values",], quote = FALSE)
              cat("\n")
            }
            if (any(c("ALL", "Phenotype") %in% what)) {
              cat("\n")
              cat("-Phenotypes: \n")
              print(object@summary$input["phenotypes",], quote = FALSE)
              cat("\n")
            }
            if (any(c("ALL", "Interactome") %in% what)) {
              cat("\n")
              cat("-Interactome: \n")
              print(object@summary$db, quote = FALSE)
              cat("\n")
            }
            if (any(c("ALL", "Para") %in% what)) {
              cat("\n")
              cat("-Parameters for analysis: \n")
              print(object@summary$para, quote = FALSE)
              cat("\n")
            }
            if (any(c("ALL", "Result") %in% what)) {
              cat("\n")
              cat("-Subnetwork identified: \n")
              print(object@summary$result, quote = FALSE)
              cat("\n")
            }
          })

setMethod("show", signature = "NWA", function(object) {
  cat("A NWA (Network Analysis) object:\n")
  summarize(object, what = c("Pval", "Phenotype", "Interactome", "Para"))
})