diff Testtest/GCMS-test_settings.R @ 0:40de28c7d3fb draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Testtest/GCMS-test_settings.R	Thu Nov 23 08:50:14 2017 -0500
@@ -0,0 +1,227 @@
+# author: Pauline Ribeyre
+
+
+#####################
+# required packages #
+#####################
+
+library("metaMS") # provides "metaMSsettings" class
+
+
+####################
+# default settings #
+####################
+
+# PeakPicking
+PeakPicking.method = "matchedFilter"
+PeakPicking.step = 0.05
+PeakPicking.steps = 2
+PeakPicking.mzdiff = 0.5
+PeakPicking.fwhm = 5
+PeakPicking.snthresh = 2
+PeakPicking.max = 500
+
+# Alignment
+# ?
+
+# CAMERA
+CAMERA.perfwhm = 1
+
+# DBconstruction
+DBconstruction.minintens = 0.0
+DBconstruction.rttol = 0.1
+DBconstruction.intensityMeasure = "maxo"
+DBconstruction.DBthreshold = .80
+DBconstruction.minfeat = 5
+
+# match2DB
+match2DB.rtdiff = 0.5
+match2DB.minfeat = 5
+# match2DB.rtval = ?
+# match2DB.mzdiff = ?
+# match2DB.ppm = ?
+match2DB.simthresh = 0.8
+match2DB.timeComparison = "rt"
+match2DB.RIdiff = 5
+
+# betweenSamples
+betweenSamples.min.class.fraction = 0.8 # pools
+# betweenSamples.min.class.fraction = 0.5 # samples
+betweenSamples.min.class.size = 5
+betweenSamples.timeComparison = "rt"
+betweenSamples.rtdiff = 0.5
+betweenSamples.RIdiff = 2 # default setting
+# betweenSamples.RIdiff = 0.05 # w4m setting
+betweenSamples.simthresh = 0.8
+
+# matchIrrelevants
+# matchIrrelevants.irrelevantClasses = c("Bleeding", "Plasticizers")
+# matchIrrelevants.RIdiff = ?
+# matchIrrelevants.rtdiff = ?
+# matchIrrelevants.simthresh = ?
+# matchIrrelevants.timeComparison = "RI"
+
+# TODO RI option
+
+
+###################
+# settings object #
+###################
+
+# settings <- metaMSsettings("protocolName" = "settings", "chrom" = "GC")
+
+settings <- metaMSsettings("protocolName" = "settings",
+                            "chrom" = "GC",
+                           
+                            PeakPicking = list(
+                              method = PeakPicking.method,
+                              step = PeakPicking.step,
+                              steps = PeakPicking.steps,
+                              mzdiff = PeakPicking.mzdiff,
+                              fwhm = PeakPicking.fwhm,
+                              snthresh = PeakPicking.snthresh,
+                              max = PeakPicking.max),
+                           
+                            CAMERA = list(perfwhm = CAMERA.perfwhm))
+
+metaSetting(settings, "DBconstruction") <- list(
+  minintens = DBconstruction.minintens,
+  rttol = DBconstruction.rttol,
+  intensityMeasure = DBconstruction.intensityMeasure,
+  DBthreshold = DBconstruction.DBthreshold, 
+  minfeat = DBconstruction.minfeat)
+
+metaSetting(settings, "match2DB") <- list(
+  simthresh = match2DB.simthresh,
+  timeComparison = match2DB.timeComparison,
+  rtdiff = match2DB.rtdiff,
+  RIdiff = match2DB.RIdiff,
+  minfeat = match2DB.minfeat)
+
+metaSetting(settings, "betweenSamples") <- list(
+  min.class.fraction = betweenSamples.min.class.fraction,
+  min.class.size = betweenSamples.min.class.size,
+  timeComparison = betweenSamples.timeComparison,
+  rtdiff = betweenSamples.rtdiff,
+  RIdiff = betweenSamples.RIdiff,    
+  simthresh = betweenSamples.simthresh)
+
+# metaSetting(GALAXY.GC, "matchIrrelevants") <- list(
+#   irrelevantClasses = matchIrrelevants.irrelevantClasses,
+#   RIdiff = matchIrrelevants.RIdiff,
+#   rtdiff = matchIrrelevants.rtdiff,
+#   simthresh = matchIrrelevants.simthresh,
+#   timeComparison = matchIrrelevants.timeComparison)
+
+
+# best settings pool
[e-mail] = 5
+settings@PeakPicking$fwhm = 6
+settings@PeakPicking$mzdiff = -0.5
[e-mail] = 0.8
[e-mail] = 0.7
[e-mail] = 0.05
+
+
+# best settings samples
[e-mail] = 5
+settings@PeakPicking$fwhm = 6
+settings@PeakPicking$mzdiff = 0.5
[e-mail] = 0.5
[e-mail] = 0.7
[e-mail] = 0.05
+
+
+#################
+# vary settings #
+#################
+
+pop <- function(list) {
+  # Removes the last item from a list.
+  #
+  # Args:
+  #   list: the list to pop.
+  #
+  # Returns:
+  #   The last item of the list before it was removed.
+  
+  val <- list[length(list)]
+  assign(as.character(substitute(list)), list[-length(list)], parent.frame())
+  return (val)
+  
+}
+
+
+vary_list_to_settings <- function(settings, vary_list, title = "", titles_to_test = c(), settings_to_test = c()) {
+  # Reads the list of parameters to vary and their ranges and builds a list of file titles and settings from it.
+  #
+  # Args:
+  #   settings: default settings for runGC.
+  #   vary_list: list of parameters to vary and the values each parameter must take.
+  #   title: title of the current file (concatenation of the values taken by the varied parameters).
+  #   titles_to_test:  list of titles (one for each settings set) (concatenation of the values taken by the varied parameters).
+  #   settings_to_test: list of settings sets for runGC.
+  #
+  # Returns:
+  #   A list containing:
+  #   1: the list of file titles ;
+  #   2: the list of runGC() settings.
+  
+  if (length(vary_list) == 0) { # if there are no parameters to vary
+    
+    titles_to_test <- c(titles_to_test, "default_settings")
+    settings_to_test <- c(settings_to_test, settings)
+    
+  }
+  
+  else {
+    
+    param <- pop(vary_list)[[1]]
+    
+    title <- paste0(title, param[1])
+    setting <- param[2]
+    range <- as.numeric(param[3:length(param)])
+    
+    # for each possible value of the parameter
+    for (p in range) {
+      
+      # change the settings
+      isSlot <- regexpr("\\$", setting)[1]
+      
+      if (isSlot == -1) { # the parameter is a slot in class metaMSsettings
+        slot(settings, setting) <- p
+      }
+      else { # the parameter is not a slot in class metaMSsettings
+        slot(settings, substr(setting, 1, isSlot - 1))[substr(setting, isSlot + 1, nchar(setting))] <- p
+      }
+      
+      new_title <- paste0(title, "=", p, "_")
+      
+      # save the settings in a list
+      if (length(vary_list) == 0) {
+        titles_to_test <- c(titles_to_test, new_title)
+        settings_to_test <- c(settings_to_test, settings)
+      }
+      else {
+        res <- vary_list_to_settings(settings, vary_list, new_title, titles_to_test, settings_to_test)
+        titles_to_test <- res[[1]]
+        settings_to_test <- res[[2]]
+      }
+      
+    } # end for
+    
+  } # end else
+  
+  return (list(titles_to_test, settings_to_test))
+  
+}
+
+
+############
+#   main   #
+############
+
+# settings to vary and ranges of values
+res <- vary_list_to_settings(settings, vary_list)
+titles_to_test <- res[[1]]
+settings_to_test <- res[[2]]