R/comp_generate_options.R

In YasinEl/mzRAPP: Benchmark Dataset Generation and Non-Targeted Data Pre-Processing Assessment

#' generate_options
#'
#' @param raw_b_table raw_b_table
#' @param algo algo
#'
#' @importFrom data.table data.table
#'
#' @keywords internal
generate_options <- function(raw_b_table, algo){
  #Hardcoded internal columns
  if("peaks.rt_weig" %in% colnames(raw_b_table)) {
    rt_measure <- "peaks.rt_weig"
  } else {
    rt_measure <- "peaks.rt_raw"
  }
  columns_dt <- data.table('internal_columns' = c('peak_height', 'peak_area', 'sample_name','molecule', 'adduct', 'isoab', 'mz_exact',
                                                  'rt_start', 'rt_end', 'rt', 'mz', 'comp_id', 'mz_start', 'mz_end'),
                           'b_columns' = c('peaks.height', 'peaks.area', 'FileName', 'molecule', 'adduct', 'isoab', 'mz_ex',
                                           'peaks.StartTime', 'peaks.EndTime', rt_measure, 'peaks.mz_accurate', 'IDX', 'peaks.mz_min', 'peaks.mz_max')
                           )
  #Get sample names from benchmark
  samples_dt <- data.table('sample_id' = seq(unique(raw_b_table$FileName)),
                           'b_samples' = sort(unique(raw_b_table$FileName)))
  switch(algo,
    'XCMS' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'sample_name', 'rt_start', 'rt_end', 'rt', 'mz', 'mz_start', 'mz_end'),
                                                 'ug_columns' = c('maxo', 'into', 'sample', 'rtmin', 'rtmax', 'rt', 'mz', 'mzmin', 'mzmax')),
                          all.x = TRUE, by=c('internal_columns'))
      #Add g columns
            columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                       'g_columns' = c('rt', 'mz')),
                                all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := sample_id]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := ifelse(grepl('^[0-9]', b_samples), paste0('X', b_samples), b_samples)]
    },
    'XCMS3' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'sample_name', 'rt_start', 'rt_end', 'rt', 'mz', 'mz_start', 'mz_end'),
                                                 'ug_columns' = c('maxo', 'into', 'sample', 'rtmin', 'rtmax', 'rt', 'mz', 'mzmin', 'mzmax')),
                          all.x = TRUE, by=c('internal_columns'))
      #Add g columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                 'g_columns' = c('rtmed', 'mzmed')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := sample_id]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := b_samples]
    },
    'SLAW' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'rt_start', 'rt_end', 'rt', 'mz', 'mz_start', 'mz_end'),
                                                 'ug_columns' = c('height', 'intensity', 'rt_min', 'rt_max', 'rt', 'mz', 'mz_min', 'mz_max')),
                          all.x = TRUE, by=c('internal_columns'))
      #Add g columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                 'g_columns' = c('mean_rt', 'mean_mz')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := b_samples]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := b_samples]
    },
    'Metaboanalyst' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'sample_name', 'rt_start', 'rt_end', 'rt', 'mz', 'mz_start', 'mz_end'),
                                                 'ug_columns' = c('maxo', 'into', 'sample', 'rtmin', 'rtmax', 'rt', 'mz', 'mzmin', 'mzmax')),
                          all.x = TRUE, by=c('internal_columns'))
      #Add g columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                 'g_columns' = c('rt', 'mz')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := sample_id]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := tools::file_path_sans_ext(b_samples)]
    },
'CompoundDiscoverer' = {
  #Add ug columns
  columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'sample_name', 'rt_start', 'rt_end', 'rt', 'mz'),
                                             'ug_columns' = c('Apex Intensity', 'Area', 'Study File ID', 'Left RT [min]', 'Right RT [min]', 'Apex RT [min]', 'Apex mz')),
                      all.x = TRUE, by=c('internal_columns'))
  #Add g columns
  columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                             'g_columns' = c('rt', 'mz')),
                      all.x = TRUE, by=c('internal_columns'))

  #Add ug samples
  samples_dt <- samples_dt[, 'ug_samples' := sample_id]
  #Add g samples
  samples_dt <- samples_dt[, 'g_samples' := ifelse(grepl('^[0-9]', b_samples), paste0('X', b_samples), b_samples)]
},
    'El-MAVEN' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'sample_name', 'rt_start', 'rt_end', 'rt', 'mz', 'mz_start', 'mz_end'),
                                                 'ug_columns' = c('peakIntensity', 'peakAreaTopCorrected', 'sample', 'rtmin', 'rtmax', 'rt', 'peakMz', 'mzmin', 'mzmax')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add g columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                 'g_columns' = c('medRt', 'medMz')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := b_samples]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := b_samples]


    },
    'MS-DIAL' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'rt_start', 'rt_end', 'rt', 'mz'),
                                                 'ug_columns' = c('Height', 'Area', 'RT left(min)', 'RT right (min)', 'RT (min)', 'Precursor m/z')),
                          all.x = TRUE, by=c('internal_columns'))
      #Add g columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                 'g_columns' = c('Average Rt(min)', 'Average Mz')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := b_samples]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := b_samples]
    },
    'OpenMS' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_area', 'rt_start', 'rt_end', 'rt', 'mz'),
                                                 'ug_columns' = c('intensity', 'rt_start', 'rt_end', 'rt', 'mz')),
                          all.x = TRUE, by=c('internal_columns'))
      #Add g columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                 'g_columns' = c('rt_cf', 'mz_cf')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := b_samples]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := b_samples]
    },
    'MZmine 2' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'rt_start', 'rt_end', 'rt', 'mz', 'mz_start', 'mz_end'),
                                                 'ug_columns' = c('Peak height', 'Peak area', 'Peak RT start', 'Peak RT end', 'Peak RT', 'Peak m/z', 'Peak m/z min', 'Peak m/z max')),
                          all.x = TRUE, by=c('internal_columns'))
      #Add g columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                 'g_columns' = c('row retention time', 'row m/z')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := b_samples]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := b_samples]
    },
    'MZmine 3' = {
      #Add ug columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('peak_height', 'peak_area', 'rt_start', 'rt_end', 'rt', 'mz', 'mz_start', 'mz_end'),
                                                 'ug_columns' = c('Peak height', 'Peak area', 'Feature RT start', 'Feature RT end', 'Feature RT', 'Feature m/z', 'Feature m/z min', 'Feature m/z max')),
                          all.x = TRUE, by=c('internal_columns'))
      #Add g columns
      columns_dt <- merge(columns_dt, data.table('internal_columns' = c('rt', 'mz'),
                                                 'g_columns' = c('row retention time', 'row m/z')),
                          all.x = TRUE, by=c('internal_columns'))

      #Add ug samples
      samples_dt <- samples_dt[, 'ug_samples' := b_samples]
      #Add g samples
      samples_dt <- samples_dt[, 'g_samples' := b_samples]
    },
{return(NULL)})

  #Find smaller column and pad it with NA
  if(nrow(samples_dt) > nrow(columns_dt)){
    diff = nrow(samples_dt) - nrow(columns_dt)
    for (i in 1:diff){
      columns_dt <- rbind(columns_dt, columns_dt[NA])
    }
  } else if(nrow(columns_dt) > nrow(samples_dt)){
    diff = nrow(columns_dt) - nrow(samples_dt)
    for (i in 1:diff){
      samples_dt <- rbind(samples_dt, samples_dt[NA])
    }
  }

  options_dt <- cbind(columns_dt, samples_dt)
  return(options_dt)
}