R/MIGSAres-class.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' MIGSAres S4 class implementation in R
#'
#' This S4 class represents the results of one MIGSA execution in R.
#'
#' @importFrom data.table data.table
#' @name MIGSAres-class
#' @rdname MIGSAres-class
#' @seealso \code{\link{MIGSA}}
#' @seealso \code{\link{getAdditionalInfo}}
#' @seealso \code{\link{MIGSAres-common}}
#' @seealso \code{\link{MIGSAres-genes}}
#' @seealso \code{\link{MIGSAres-GOanalysis}}
#' @seealso \code{\link{MIGSAres-plots}}
#' @seealso \code{\link{setEnrCutoff}}
#' @seealso \code{\link{summary}}
#' @exportClass MIGSAres
#'
setClass(
  Class = "MIGSAres",
  slots = c(
    migsa_res_all = "data.table",
    migsa_res_summary = "data.frame",
    enr_cutoff = "numeric",
    genes_rank = "list"
  ),
  prototype = list(
    enr_cutoff = as.numeric(NA)
  ),
  validity = function(object) {
    # check that data frames are correct
    migsa_res_all_ok <- all(colnames(object@migsa_res_all) %in%
      c(
        "experiment_name", "gene_set_name", "id", "name", "SEA_GS_genes",
        "SEA_enriched", "SEA_score", "SEA_pval", "SEA_enriching_genes",
        "GSEA_GS_genes", "GSEA_enriched", "GSEA_score", "GSEA_pval",
        "GSEA_enriching_genes", "is_GO"
      ))
    migsa_res_all_ok <- migsa_res_all_ok &&
      (ncol(object@migsa_res_all) == 15)

    migsa_res_summary_ok <- all(c("id") %in%
      colnames(object@migsa_res_summary))

    enr_cutoff_ok <- is.na(object@enr_cutoff) ||
      (0 <= object@enr_cutoff && object@enr_cutoff <= 1)
    genes_rank_ok <- all(unlist(lapply(
      object@genes_rank, is,
      "data.frame"
    )))

    return(migsa_res_all_ok && enr_cutoff_ok &&
      migsa_res_summary_ok && genes_rank_ok)
  }
)