R/fct_parseDelimitedMS.R

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

#' Parse Delimited MS files with fread and MALDIquant
#'
#' @param proteinPaths proteinPaths 
#' @param proteinNames proteinNames 
#' @param smallMolPaths smallMolPaths 
#' @param smallMolNames smallMolNames names of the 
#' @param centroid Do the files contain profile or centroid data (currently implemented as just
#'     one TRUE/FALSE, but could mappply) 
#' @param exportDirectory Where will mzml files be written?
#'
#' @return sample-named vector of filpaths of random-named mzml files
#' @export 
#'
delim_to_mzml <- function(proteinPaths,
                          proteinNames,
                          smallMolPaths,
                          smallMolNames,
                          exportDirectory,
                          centroid){
  
  if (length(proteinPaths) != length(proteinNames)) {
    stop("unequal proteinPaths and proteinNames")
  }
  if (length(smallMolPaths) != length(smallMolNames)) {
    stop("unequal proteinPaths and proteinNames")
  }
  
  
  combPaths <- c(proteinPaths,
                 smallMolPaths)
  combPaths <- unlist(combPaths)
  
  combNames <- c(proteinNames, 
                 smallMolNames)
  combNames <- unlist(combNames)
  
  # Read delim files, for now just regular mass then intensity columns
  importedFiles <- lapply(combPaths, 
                          function(x){ 
                            a <- data.table::fread(x)
                            MALDIquant::createMassSpectrum(mass = a[[1]],
                                                           intensity = a[[2]])
                          })
  
  
  mzFilePaths <- sapply(seq_along(unique(combNames)),
                        function(x) {
                          paste0(tempfile(tmpdir = exportDirectory),
                                 fileext = ".mzml")
                        })
  
  mzFilePaths <- normalizePath(mzFilePaths, 
                               mustWork = FALSE,
                               winslash = "/")
  
  
  key <- base::split(importedFiles, combNames)
  names(mzFilePaths) <- names(key)
  
  lengthProgress <- length(key)
  count <- 0
  
  # withProgress doesn't currently work outside shiny
  if (!is.null(shiny::getDefaultReactiveDomain())) { 
    withProgress(message = 'Conversion in progress',
                 detail = 'This may take a while...', value = 0, {
                   
                   for (i in seq_along(key)) {
                     incProgress(1/lengthProgress)
                     
                     MALDIquantForeign::exportMzMl(x = as.list(key[[i]]),
                                                   path = mzFilePaths[[i]],
                                                   force = TRUE)
                     
                   }
                 })
    
  } else {
    for (i in seq_along(key)) {
      
      MALDIquantForeign::exportMzMl(x = as.list(key[[i]]),
                                    path = mzFilePaths[[i]],
                                    force = TRUE)
      
    }
  }
  
  
  return(mzFilePaths)
  
}