R/GSEAres.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' @include GenesetRes.R
GSEAres <- setClass(
  Class = "GSEAres",
  slots = c(
    gene_sets_res = "list"
  ),
  prototype = list(),
  validity = function(object) {
    gene_sets_res_ok <- all(unlist(lapply(object@gene_sets_res, function(x) {
      is(x, "GenesetRes")
    })))

    return(gene_sets_res_ok)
  }
)

#' @importFrom data.table as.data.table data.table setkey
as.data.table.GSEAres <- function(x, ...) {
  # convert each gene set result to character vector
  to <- do.call(rbind, lapply(x@gene_sets_res, function(res) {
    actInfo <- asCharacter(res)
    return(actInfo)
  }))

  if (is.null(to)) {
    return(
      data.table(
        id = character(),
        name = character(),
        GSEA_enriched = logical(),
        GSEA_score = logical(),
        GSEA_pval = logical(),
        GSEA_enriching_genes = character(),
        GSEA_GS_genes = character()
      )
    )
  }

  # make it a data.table and put the colnames
  to <- data.table(to)
  colnames(to) <- c(
    "id", "name", "GSEA_enriched", "GSEA_score",
    "GSEA_pval", "GSEA_enriching_genes",
    "GSEA_GS_genes"
  )

  # set data.table keys, to merge faster
  setkey(to, id, name)

  return(to)
}

setGeneric(name = "gene_sets_res", def = function(object) {
  standardGeneric("gene_sets_res")
})

setMethod(
  f = "gene_sets_res", signature = "GSEAres",
  definition = function(object) {
    return(object@gene_sets_res)
  }
)