R/9_hmdb_database.R

In tidymass/metpath: Pathway analysis for metabolomics data

#' #' @title get_hmdb_pathway
#' #' @description Get compound from HMDB (SMPDB)
#' #' @author Xiaotao Shen
#' #' \email{shenxt1990@@outlook.com}
#' #' @param threads threads
#' #' @export
#' 
#' get_hmdb_compound <- function(threads = 3) {
#'   data("hmdb_compound_database", envir = environment())
#'   message(
#'     crayon::yellow(
#'       "This database is downloaded in",
#'       hmdb_compound_database@database.info$Version
#'     )
#'   )
#'   # cat("\n")
#'   return(hmdb_compound_database)
#' }


#' #' @title get_hmdb_pathway
#' #' @description Get pathways from HMDB (SMPDB)
#' #' @author Xiaotao Shen
#' #' \email{shenxt1990@@outlook.com}
#' #' @param threads threads
#' #' @export
#' # load("data/hmdb_pathway.rda")
#' # load("data/primary_pathway")
#' #
#' # idx = match(primary_pathway, hmdb_pathway@pathway_id)
#' # idx = idx[!is.na(idx)]
#' # pathway_class =
#' #   hmdb_pathway@pathway_class
#' #
#' # for(x in idx){
#' #   pathway_class[[x]] = paste(pathway_class[[x]],
#' #   "primary_pathway", sep = ";")
#' # }
#' #
#' #
#' #
#' # pathway_class[idx]
#' #
#' # hmdb_pathway@pathway_class = pathway_class
#' #
#' # save(hmdb_pathway, file = "data/hmdb_pathway.rda", )
#' 
#' get_hmdb_pathway <-
#'   function(threads = 3) {
#'     data("hmdb_pathway", envir = environment())
#'     message(
#'       crayon::yellow(
#'         "This database is downloaded in",
#'         hmdb_pathway@database_info$version
#'       )
#'     )
#'     # cat("\n")
#'     return(hmdb_pathway)
#'   }