R/trans_id.R

In ropensci/DoOR.functions: Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome

#' trans_id
#' 
#' Translate chemical identifiers from one to the other.
#' 
#' @param x character vector, one or many chemical identifiers
#' @param from character, the type of identifier to translate from (one of the
#'   column names of ``odor``)
#' @param to character, the type of identifier to translate from (one of the
#'   column names of ``odor``)
#' @param odor_data the data frame containing the odor information (defaults to
#'   ``odor``).
#'   
#' @return character vector of translated chemical identifiers
#' @export
#' @aliases transID trans_id
#'   
#' @examples
#' # load data
#' library(DoOR.data)
#' 
#' # transform CAS to InChIKey
#' trans_id("123-92-2")
#' 
#' # transform Name to InChIKey
#' trans_id("isopentyl acetate", "Name")
#' 
#' # transform SMILE to InChIKey
#' trans_id("C(C(C)C)COC(=O)C", "SMILES", "Name")
#' 
trans_id <-
  function(x,
           from = "CAS",
           to = "InChIKey",
           odor_data = door_default_values("odor")) {
    result <- odor_data[match(x, odor_data[, from]), to]
    if (length(result) == 0) {
      warning("No match, returning NA.")
      return(NA)
    }
    return(as.character(result))
  }