R/deprecated_function4databaseClass.R

In jaspershen/metID: Metabolite identification based on MS1 and MS2 spectra

#' @title Get MS2 spectra of peaks from databaseClass object
#' @description Get MS2 spectra of peaks from databaseClass object.
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param lab.id The lab ID of metabolite.
#' @param database Database (databaseClass object).
#' @param polarity positive or negative.
#' @param ce Collision value.
#' @importFrom crayon red yellow green bgRed
#' @importFrom stringr str_detect str_extract
#' @importFrom readr cols
#' @importFrom pbapply pblapply
#' @return A MS2 spectrum (data.frame).
#' @export
#' @seealso The example and demo data of this function can be found
#' https://jaspershen.github.io/metID/articles/metID.html

getMS2spectrum = function(lab.id,
                          database,
                          polarity = c("positive", "negative"),
                          ce = "30") {
  cat(crayon::yellow(
    "`getMS2spectrum()` is deprecated, use `get_ms2_spectrum()`."
  ))
  polarity <- match.arg(polarity)
  if (class(database) != "databaseClass") {
    stop("The database must be databaseClass object.\n")
  }
  pol <- ifelse(polarity == "positive", 1, 2)
  temp <-
    database@spectra.data[[pol]][[match(lab.id, names(database@spectra.data[[pol]]))]]
  temp[[match(ce, names(temp))]]
}