R/getmzPntrs.R

In singjc/mstools: OpenSWATH Mass Spectrometry Data Exploration

#' Get a list of mz Objects 
#' @param dataPath data path that contains mzml folder of chromtogram files
#' @param runs A list variable containing paths to chromatogram files
#' @return (A list of mzRpwiz)
#' 
#' @importFrom tictoc tic toc
#' 
#' @export
getmzPntrs <- function( dataPath, runs  ){
  
  ## TODO: Make this more versatile or something
  ##*******************************
  ## Pre-Load mzML Files
  ##*******************************
  
  global <- list()
  global$chromFile <- list.files(dataPath, pattern = ".mzML$", recursive = T, full.names = T)
  names(global$chromFile) <- basename(global$chromFile)
  
  ## Get filenames from osw files and check if names are consistent between osw and mzML files. ######
  filenames <- DIAlignR::getRunNames( dataPath, oswMerged=TRUE)
  # runs <- c(input$Reference, gsub('...........$', '', input$ChromatogramFile[,'name']))
  filenames <- filenames[filenames$runs %in% runs,]
  #filenames <- filenames[grepl(paste(filenames$runs, collapse = "|"), names(global$chromFile)),]
  tictoc::tic('Pre-Loading mzML Chromatogram Files onto disk')
  mzPntrs <- list()
  for ( chromatogram_input_index_num in seq(1, length(filenames$runs)) ){
    tryCatch(
      expr = {
        tictoc::tic()
        run <- rownames(filenames)[ chromatogram_input_index_num ]
        current_filename <- filenames$runs[ chromatogram_input_index_num ]
        # message(sprintf("\rCacheing mzML for %s of %s runs", run, length(filenames$runs)))
        ## Get path for current chromatogram file
        chromatogram_file_i <-  global$chromFile[ grepl(current_filename, names(global$chromFile)) ][[1]]
        # Create an mzR object that stores all header information, and use ProteoWizard api to access data from MzML file
        mz <- mzR::openMSfile(chromatogram_file_i, backend = "pwiz", verbose = T)
        ## Get table of chromatogram incidces and respective transtion ids
        chromHead <- mzR::chromatogramHeader(mz)
        ## Store run id and mz object into master list
        mzPntrs[[run]] <- list()
        mzPntrs[[run]]$mz <- mz
        mzPntrs[[run]]$chromHead <- chromHead
        ## End timer
        exec_time <- tictoc::toc(quiet = T)
        message(sprintf("\rCacheing mzML for %s of %s runs: Elapsed Time = %s sec", run, length(filenames$runs), round(exec_time$toc - exec_time$tic, 3) ))
      },
      error = function(e){
        message(sprintf("[getmzPntrs] There was an issue cacheing %s, skipping...: %s\n", current_filename, e$message))
      }
    ) # End tryCatch
  }
  tictoc::toc()
  
  return( mzPntrs )
  
}