R/parseDelimitedMS.R

In chasemc/tempRepo: Protein and small molecule analysis of bacteria by MALDI-TOF MS

#' parseDelimitedMS
#'
#' @param proteinPaths proteinPaths 
#' @param proteinNames proteinNames 
#' @param smallMolPaths smallMolPaths 
#' @param smallMolNames smallMolNames 
#' @param centroid centroid 
#' @param exportDirectory NA
#'
#' @return NA
#' @export
#'
parseDelimitedMS <- function(proteinPaths,
                             proteinNames,
                             smallMolPaths,
                             smallMolNames,
                             exportDirectory,
                             centroid){
  
  req(length(proteinPaths) == length(proteinNames))
  req(length(smallMolPaths) == length(smallMolNames))
  
  
  tempRepo::popup3()
  
  combPaths <- c(proteinPaths,
                 smallMolPaths)
  
  #lapply in case someone provides different file types at same time -_-
  importedFiles <- unlist(lapply(combPaths, 
                             function(x) 
                               MALDIquantForeign::import(x,
                                                         centroided = as.logical(centroid))))

  combNames <- c(proteinNames, 
                 smallMolNames)
  
  mzFilePaths <- file.path(exportDirectory,
                          paste0(combNames,
                                 ".mzML"))
  
  mzFilePaths <- normalizePath(mzFilePaths, 
                             mustWork = FALSE)
  
  key <- base::split(importedFiles, mzFilePaths)
  
  
  lengthProgress <- length(key)
  count <- 0
  
  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 = names(key)[[i]],
                                                 force = TRUE)
                   
                 }
                 
                 
               })
  return(list(mzFilePaths = mzFilePaths,
              sampleIds = combNames))
  
}