fix for research data without Z-scores in DIMS

Author: mraves2

DIMS/CollectFilled.R

@@ -28,6 +28,8 @@ for (scanmode in scanmodes) {
   # calculate Z-scores
   if (z_score == 1) {
     outlist_stats <- calculate_zscores_peakgrouplist(outlist_total)
+  } else {
+    outlist_stats <- outlist_total
   }
   # calculate ppm deviation
   outlist_withppm <- calculate_ppm_deviation(outlist_stats)

DIMS/GenerateQCOutput.R

@@ -37,9 +37,11 @@ dir.create(paste0(outdir, "/plots"), showWarnings = FALSE)
 control_label <- "C"
 
 #### CHECK NUMBER OF CONTROLS ####
-file_name <- "Check_number_of_controls.txt"
-min_num_controls <- 25
-check_number_of_controls(outlist, min_num_controls, file_name)
+if (any(grepl("nr_ctrls", colnames(outlist)))) {
+  file_name <- "Check_number_of_controls.txt"
+  min_num_controls <- 25
+  check_number_of_controls(outlist, min_num_controls, file_name)
+}
 
 #### INTERNAL STANDARDS ####
 is_list <- outlist[grep("Internal standard", outlist[, "relevance"], fixed = TRUE), ]

DIMS/preprocessing/collect_filled_functions.R

@@ -129,9 +129,13 @@ order_columns_peakgrouplist <- function(peakgroup_list) {
 
   original_colnames <- colnames(peakgroup_list)
   mass_columns <- c(grep("mzm", original_colnames), grep("nrsamples", original_colnames))
-  descriptive_columns <- grep("assi_HMDB", original_colnames):grep("avg.int", original_colnames)
+  if (any(grepl("avg.int", original_colnames))) {
+    descriptive_columns <- grep("assi_HMDB", original_colnames):grep("avg.int", original_colnames)
+  } else {
+    descriptive_columns <- grep("assi_HMDB", original_colnames):grep("ppmdev", original_colnames)
+  }
   intensity_columns <- c((grep("nrsamples", original_colnames) + 1):(grep("assi_HMDB", original_colnames) - 1))
-  # if no Z-scores have been calculated, the following two variables will be empty without consequences for outlist_total
+  # if no Z-scores have been calculated, the following two variables will be empty without consequences for peakgroup_list
   control_columns <- grep ("ctrls", original_colnames)
   zscore_columns <- grep("_Zscore", original_colnames)
   # create peak group list with columns in correct order

DIMS/preprocessing/sum_intensities_adducts.R

@@ -32,8 +32,8 @@ sum_intensities_adducts <- function(peakgroup_list, hmdb_part, adducts, z_score)
     int_cols_pats <- grep("P", colnames(peakgroup_list)[1:which(colnames(peakgroup_list) == "avg.ctrls")])
     int_cols <- c(int_cols_ctrls, int_cols_pats)
   } else {
-    int_cols_start <- which(colnames(peakgroup_list) == "nrsamples") + 1
-    int_cols_end <- which(colnames(peakgroup_list) == "assi_HMDB") - 1
+    int_cols_start <- which(colnames(peakgroup_list) == "ppmdev") + 1
+    int_cols_end <- ncol(peakgroup_list)
     int_cols <- c(int_cols_start:int_cols_end)
   }