comments/TODOs on chromatographic mass interval #1

fgcz · Oct 23, 2020 · e1580fb · e1580fb
1 parent 592aa2f
commit e1580fb
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/R/rawR.R b/R/rawR.R
@@ -347,7 +347,7 @@ readSpectrum <- function(rawfile, scan = NULL, tmpdir=tempdir(), validate=FALSE)
 #' # Example 1: not meaning full but proof-of-concept
 #' (rawfile <- file.path(path.package(package = 'rawR'), 'extdata', 'sample.raw'))
 #' 
-#' X <- readChromatogram(rawfile, mass=c(669.8381, 726.8357), tol=1000)
+#' C <- readChromatogram(rawfile, mass=c(669.8381, 726.8357), tol=1000)
 #' 
 #' # Example 2: extract iRT peptides
 #' iRTpeptide <- c("LGGNEQVTR", "YILAGVENSK", "GTFIIDPGGVIR", "GTFIIDPAAVIR",
@@ -432,13 +432,14 @@ readChromatogram <- function(rawfile,
         #message(length(rv))
         rv <- lapply(rv,
                      function(x){
+                         x$type <- type
                          x$filename <- rawfile
                          x$tol <- tol
                          x$filter <- filter
                          # x$times.max <- x$times[which.max(x$intensities)][1]
                          class(x) <- c(class(x), 'rawRchromatogram');
                          x})
-        class(rv) <- 'rawRchromatogramSet'
+
     }else{
         if (mono){
             rvs <- system2("mono", args = c(shQuote(exe), shQuote(rawfile), "chromatogram", shQuote(filter)), stdout=tfstdout)
@@ -448,6 +449,7 @@ readChromatogram <- function(rawfile,
         rv <- read.csv(tfstdout, header = TRUE, comment.char = "#")
     }
     unlink(c(tfi, tfo, tfstdout))
+    class(rv) <- 'rawRchromatogramSet'
     rv
 }
 

diff --git a/src/rawR.cs b/src/rawR.cs
@@ -609,17 +609,28 @@ private static void Main(string[] args)
             /// <param name="outputData">
             /// The output data flag.
             /// </param>
+            /// <param name="filter">
+            /// The chromatic filter flag.
+            /// </param>
             private static void GetChromatogram(IRawDataPlus rawFile, int startScan, int endScan, bool outputData, string filter = "ms")
             {
 	        if (IsValidFilter(rawFile, filter) == false){
                     Console.WriteLine("# '{0}' is not a valid filter string.", filter);
 		    return;
 	        }
 
+		// TODO([email protected]): check mass interval for chromatograms and its dep for diff MS detector types
+		// TODO([email protected]): return mass intervals to the R enviroment
                 // Define the settings for getting the Base Peak chromatogram
                 ChromatogramTraceSettings settingsTIC = new ChromatogramTraceSettings(TraceType.TIC){Filter=filter};
-                ChromatogramTraceSettings settingsBasePeak = new ChromatogramTraceSettings(TraceType.BasePeak){Filter=filter};
-                ChromatogramTraceSettings settingsMassRange = new ChromatogramTraceSettings(TraceType.MassRange){Filter=filter};
+                ChromatogramTraceSettings settingsBasePeak = new ChromatogramTraceSettings(TraceType.BasePeak){
+			Filter=filter,
+                        MassRanges = new[] {ThermoFisher.CommonCore.Data.Business.Range.Create(100, 1805)}
+			};
+                ChromatogramTraceSettings settingsMassRange = new ChromatogramTraceSettings(TraceType.MassRange){
+        		Filter=filter,
+                        MassRanges = new[] {ThermoFisher.CommonCore.Data.Business.Range.Create(50, 2000000)}
+			};
 
                 // Get the chromatogram from the RAW file. 
                 var dataTIC = rawFile.GetChromatogramData(new IChromatogramSettings[] {settingsTIC}, startScan, endScan);
@@ -638,12 +649,12 @@ private static void GetChromatogram(IRawDataPlus rawFile, int startScan, int end
                     Console.WriteLine("# Base Peak chromatogram ({0} points)", traceBasePeak[0].Length);
                     Console.WriteLine("# MassRange chromatogram ({0} points)", traceMassRange[0].Length);
 
-                    Console.WriteLine("scan,rt,intensity.BasePeak,intensity.TIC,intensity.MassRange");
+                    Console.WriteLine("rt,intensity.BasePeak,intensity.TIC,intensity.MassRange");
                     if (outputData)
                     {
                         for (int i = 0; i < traceBasePeak[0].Length; i++)
                         {
-                            Console.WriteLine("{0},{1:F3},{2:F0},{3:F0},{4:F0}", i, traceBasePeak[0].Times[i], traceBasePeak[0].Intensities[i], traceTIC[0].Intensities[i], traceMassRange[0].Intensities[i]);
+                            Console.WriteLine("{1:F3},{2:F0},{3:F0},{4:F0}", i, traceBasePeak[0].Times[i], traceBasePeak[0].Intensities[i], traceTIC[0].Intensities[i], traceMassRange[0].Intensities[i]);
                         }
                     }
                 }