R/IGSAres.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' @include GenesetsRes.R
IGSAres <- setClass(
  Class = "IGSAres",
  slots = c(
    name = "character",
    gene_sets_res = "list",
    genes_rank = "data.frame"
  ),
  prototype = list(
    genes_rank = data.frame()
  ),
  validity = function(object) {
    # gene_sets_res is a list of GenesetsRes
    gene_sets_res_ok <- all(unlist(lapply(
      object@gene_sets_res,
      function(x) is(x, "GenesetsRes")
    )))
    return(gene_sets_res_ok)
  }
)

# to avoid R CMD check errors we set them as NULL
experiment_name <- gene_set_name <- NULL
#' @importFrom data.table as.data.table data.table setkey
#' @include GenesetsRes.R
as.data.table.IGSAres <- function(x, ...) {
  # convert to data.table each GenesetsRes
  to <- do.call(rbind, lapply(x@gene_sets_res, function(gsetsRes) {
    actRes <- as.data.table(gsetsRes)
    return(actRes)
  }))

  # add some IGSA information
  to <- data.table(experiment_name = x@name, to)
  # set this keys for faster merging
  setkey(to, experiment_name, gene_set_name, id, name)

  return(to)
}

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

setMethod(
  f = "genes_rank", signature = "IGSAres",
  definition = function(object) {
    return(object@genes_rank)
  }
)