R/get_db.R

In johannesnicolaus/ASURAT_source: Assisting Interpretable Classifications in Single-cell Transcriptomics

#' Title
#'
#' @param db
#' @param orgdb
#' @param category_names
#' @param all_geneIDs
#'
#' @return
#' @export
#'
#' @examples
get_db <- function(db, orgdb, category_names = c("PATHID"), all_geneIDs){

  if (!(db %in% c("DO", "CO", "GO", "KEGG", "Reactome"))) {
    stop('db has to be one of: "DO", "CO", "GO", "KEGG", "Reactome"')
  }

  if (db == "CO") {
    out_db <- get_CO(orgdb)
  } else if (db == "GO") {
    out_db <- get_GO(orgdb, all_geneIDs)
  } else if (db == "KEGG") {
    out_db <- get_KEGG(orgdb)
  } else if (db == "Reactome") {
    out_db <- get_reactome(orgdb, category_names)
  }

  return(out_db)

}