R/mz_iso_annotate.R

In wmoldham/mzrtools.dev: Make Molecular Formulas Useful for Mass Spectrometry Applications

#' Annotate isotope table
#'
#' \code{mz_iso_annotate} generates a tibble enumerating all possible isotopes of
#'     a molecule and annotates this with the mass or m/\emph{z} of each isotope
#'     based on the polarity setting and the nominal mass shift of the isotope.
#'
#' @inheritParams mz_atomize
#' @inheritParams mz_calculate
#'
#' @return A named list containing the molecule elements, stable isotopes, scan
#'     polarity, and a tibble of annotated isotope information.
#'
#' @export
#'
#' @examples
#' mz_iso_annotate("C5H8O5")
#' mz_iso_annotate("C5H8O5", polarity = "negative")
#'
mz_iso_annotate <- function(molecule, polarity = "negative") {

  if (polarity %nin% c("neutral", "positive", "negative")) {
    stop("Unrecognized polarity")
  }

  elements <- mz_atomize(molecule = molecule)
  isotopes <- elements[names(elements) %in% names(iso_info)]

  # get unlabeled mass
  no_label <- elements[names(elements) %nin% names(iso_info)]
  if (length(no_label) == 0) {
    unlabeled_mass <- 0
  } else {
    no_label <- stringr::str_c(names(no_label), no_label, collapse = "")
    unlabeled_mass <- mz_calculate(molecule = no_label, polarity = polarity)
  }

  # get isotope information

  # extractor function for iso_info
  annot <- function(sublist, iso_list) {
    out <- unlist(lapply(iso_info[names(isotopes)], "[[", sublist))
    names(out) <- unlist(lapply(iso_info[names(isotopes)], "[[", "isotope"))
    iso_list %*% out
  }

  iso_list <- mz_iso_list(molecule)
  iso_mass <- c(annot("mass", iso_list) + unlabeled_mass)
  iso_shift <- c(annot("shift", iso_list))

  iso_list <-
    tibble::as_tibble(iso_list) %>%
    dplyr::bind_cols(mass = iso_mass, shift = iso_shift) %>%
    dplyr::select(.data$shift, .data$mass, dplyr::everything()) %>%
    dplyr::arrange(.data$mass)

  list(elements = elements,
       isotopes = isotopes,
       polarity = polarity,
       iso_list = iso_list)

}