R/GenesetsRes.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' @include SEAres.R
#' @include GSEAres.R
GenesetsRes <- setClass(
  Class = "GenesetsRes",
  slots = c(
    gene_sets_name = "character",
    is_GO = "logical",
    sea_res = "SEAres",
    gsea_res = "GSEAres"
  ),
  prototype = list(
    is_GO = FALSE
  )
)

#' @importFrom data.table as.data.table data.table
as.data.table.GenesetsRes <- function(x, ...) {
  # convert to data.table SEA and GSEA results
  seaRes <- as.data.table(x@sea_res)
  gseaRes <- as.data.table(x@gsea_res)

  # merge them and fill the data.table with Genesets info
  to <- merge(seaRes, gseaRes, by = c("id", "name"), all = !FALSE)
  to <- data.table(gene_set_name = x@gene_sets_name, is_GO = x@is_GO, to)

  return(to)
}