R/fct_processXMLIndSpectra.R

In chasemc/IDBac_App: MALDI-TOF MS Protien and Small Molecule Analysis

#' Process spectra data for input into SQLite
#'
#' @param spectraImport maldiquant spectra list
#' @param smallOrProtein "small" or "protein" chooses which processing pipeline is used
#' @param index logical vector describing which spectraImport spectra to use
#' @param ... advanced arguments for MALDIquant, see [IDBacApp::processSmallMolSpectra()] and/or [IDBacApp::processProteinSpectra()]
#' 
#' @return environment 
#' 
#'
processXMLIndSpectra <- function(spectraImport,
                                 smallOrProtein,
                                 index,
                                 ...){
  
  env <- new.env()
  
  env$mass_vector <- lapply(spectraImport[index], 
                            function(x){
                              x <- serial(x@mass)
                              chartoRawtoCompressed(x,
                                                    compression = 0)
                            })
  
  env$max_mass <- unlist(lapply(spectraImport[index], 
                                function(x){
                                  as.integer(max(x@mass))
                                }))
  
  env$min_mass <- unlist(lapply(spectraImport[index], 
                                function(x){
                                  as.integer(min(x@mass))
                                }))
  
  # List of whole-spectrum hashes
  env$spectrum_mass_hash <- unlist(lapply(env$mass_vector, 
                                          function(x){
                                            hashR(x)
                                          }))
  
  env$spectrum_intensity <- lapply(spectraImport[index], 
                                   function(x){
                                     x <- serial(x@intensity)
                                     chartoRawtoCompressed(x,
                                                           compression = 0)
                                   })
  
  env$spectrum_intensity_hash <- unlist(lapply(env$spectrum_intensity, 
                                               function(x){
                                                 hashR(x)
                                               }))
  
  
  if (smallOrProtein == "small") {
    env$peak_matrix <- processSmallMolSpectra(input = spectraImport[index],
                                              ...)
  } else if (smallOrProtein == "protein") {
    env$peak_matrix <- processProteinSpectra(input = spectraImport[index],
                                             ...)
  }
  
  if (!MALDIquant::isMassPeaksList(env$peak_matrix)) {
    env$peak_matrix <- list(env$peak_matrix)
  }
  
  env$peak_matrix <- lapply(env$peak_matrix, function(x){
    # note: names aren't transferred to JSON
    list(mass = x@mass, 
         intensity = x@intensity, 
         snr = x@snr)
    
  })
  
  env$peak_matrix <- unlist(lapply(env$peak_matrix, 
                                   function(x)
                                     as.character(serial(x))))
  
  return(env)
  
}