R/SEAres.R

In jcrodriguez1989/MIGSA: Massive and Integrative Gene Set Analysis

#' @include GenesetRes.R
SEAres <- setClass(
  Class = "SEAres",
  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.SEAres <- 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(),
        SEA_enriched = logical(),
        SEA_score = logical(),
        SEA_pval = logical(),
        SEA_enriching_genes = character(),
        SEA_GS_genes = character()
      )
    )
  }

  # make it a data.table and put the colnames
  to <- data.table(to)
  colnames(to) <- c(
    "id", "name", "SEA_enriched", "SEA_score",
    "SEA_pval", "SEA_enriching_genes", "SEA_GS_genes"
  )

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

  return(to)
}

#' @include GSEAres.R
setMethod(
  f = "gene_sets_res", signature = "SEAres",
  definition = function(object) {
    return(object@gene_sets_res)
  }
)