R/idRefs.R

In wilsontom/q3ML: Open and Parse MRM-MS mzML Files

#' Extract mzML idRefs
#'
#' Extract all the `idRefs` in the specified `mzML` file. The `idRefs` will correspond to the individual scan events.
#'
#' @param xmlDoc a `xml` document
#' @return a character vector of all available `idRefs`
#' @keywords internal
#' @examples \dontrun{
#' library(xml2)
#' xmlDoc <- read_xml("example_file.mzML")
#' xmlRefs <- idRefs(xmlDoc)
#' head(xmlRefs)
#' [1] "TIC"                     "SRM SIC 153.01,65.271"
#' [3] "SRM SIC 153.01,67.232"   "SRM SIC 153.01,109.094"
#' [5] "SRM SIC 179.022,107.007" "SRM SIC 179.022,134.006"
#'  }

idRefs <- function(xmlDoc)
{
  if (class(xmlDoc)[1] != "xml_document") {
    stop("...xmlDoc must be an xml_documment read in using xml2::read_xml",
         call. = FALSE)
  }

  refs <- xml2::xml_find_all(xmlDoc, "//d1:offset")
  ref_names <- sapply(refs, function(x)
    (xml2::xml_attrs(x)[["idRef"]]))
  return(ref_names)
}