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1 # author: Pauline Ribeyre
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2
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3
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4 #####################
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5 # required packages #
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6 #####################
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7
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8 library("metaMS") # provides "metaMSsettings" class
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9
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10
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11 ####################
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12 # default settings #
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13 ####################
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14
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15 # PeakPicking
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16 PeakPicking.method = "matchedFilter"
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17 PeakPicking.step = 0.05
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18 PeakPicking.steps = 2
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19 PeakPicking.mzdiff = 0.5
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20 PeakPicking.fwhm = 5
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21 PeakPicking.snthresh = 2
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22 PeakPicking.max = 500
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23
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24 # Alignment
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25 # ?
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26
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27 # CAMERA
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28 CAMERA.perfwhm = 1
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29
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30 # DBconstruction
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31 DBconstruction.minintens = 0.0
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32 DBconstruction.rttol = 0.1
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33 DBconstruction.intensityMeasure = "maxo"
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34 DBconstruction.DBthreshold = .80
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35 DBconstruction.minfeat = 5
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36
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37 # match2DB
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38 match2DB.rtdiff = 0.5
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39 match2DB.minfeat = 5
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40 # match2DB.rtval = ?
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41 # match2DB.mzdiff = ?
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42 # match2DB.ppm = ?
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43 match2DB.simthresh = 0.8
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44 match2DB.timeComparison = "rt"
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45 match2DB.RIdiff = 5
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46
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47 # betweenSamples
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48 betweenSamples.min.class.fraction = 0.8 # pools
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49 # betweenSamples.min.class.fraction = 0.5 # samples
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50 betweenSamples.min.class.size = 5
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51 betweenSamples.timeComparison = "rt"
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52 betweenSamples.rtdiff = 0.5
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53 betweenSamples.RIdiff = 2 # default setting
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54 # betweenSamples.RIdiff = 0.05 # w4m setting
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55 betweenSamples.simthresh = 0.8
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56
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57 # matchIrrelevants
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58 # matchIrrelevants.irrelevantClasses = c("Bleeding", "Plasticizers")
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59 # matchIrrelevants.RIdiff = ?
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60 # matchIrrelevants.rtdiff = ?
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61 # matchIrrelevants.simthresh = ?
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62 # matchIrrelevants.timeComparison = "RI"
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63
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64 # TODO RI option
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65
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66
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67 ###################
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68 # settings object #
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69 ###################
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70
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71 # settings <- metaMSsettings("protocolName" = "settings", "chrom" = "GC")
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72
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73 settings <- metaMSsettings("protocolName" = "settings",
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74 "chrom" = "GC",
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75
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76 PeakPicking = list(
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77 method = PeakPicking.method,
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78 step = PeakPicking.step,
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79 steps = PeakPicking.steps,
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80 mzdiff = PeakPicking.mzdiff,
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81 fwhm = PeakPicking.fwhm,
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82 snthresh = PeakPicking.snthresh,
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83 max = PeakPicking.max),
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84
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85 CAMERA = list(perfwhm = CAMERA.perfwhm))
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86
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87 metaSetting(settings, "DBconstruction") <- list(
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88 minintens = DBconstruction.minintens,
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89 rttol = DBconstruction.rttol,
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90 intensityMeasure = DBconstruction.intensityMeasure,
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91 DBthreshold = DBconstruction.DBthreshold,
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92 minfeat = DBconstruction.minfeat)
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93
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94 metaSetting(settings, "match2DB") <- list(
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95 simthresh = match2DB.simthresh,
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96 timeComparison = match2DB.timeComparison,
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97 rtdiff = match2DB.rtdiff,
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98 RIdiff = match2DB.RIdiff,
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99 minfeat = match2DB.minfeat)
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100
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101 metaSetting(settings, "betweenSamples") <- list(
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102 min.class.fraction = betweenSamples.min.class.fraction,
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103 min.class.size = betweenSamples.min.class.size,
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104 timeComparison = betweenSamples.timeComparison,
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105 rtdiff = betweenSamples.rtdiff,
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106 RIdiff = betweenSamples.RIdiff,
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107 simthresh = betweenSamples.simthresh)
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108
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109 # metaSetting(GALAXY.GC, "matchIrrelevants") <- list(
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110 # irrelevantClasses = matchIrrelevants.irrelevantClasses,
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111 # RIdiff = matchIrrelevants.RIdiff,
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112 # rtdiff = matchIrrelevants.rtdiff,
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113 # simthresh = matchIrrelevants.simthresh,
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114 # timeComparison = matchIrrelevants.timeComparison)
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115
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116
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117 # best settings pool
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118 settings@betweenSamples.min.class.size = 5
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119 settings@PeakPicking$fwhm = 6
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120 settings@PeakPicking$mzdiff = -0.5
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121 settings@betweenSamples.min.class.fraction = 0.8
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122 settings@betweenSamples.simthresh = 0.7
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123 settings@betweenSamples.rtdiff = 0.05
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124
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125
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126 # best settings samples
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127 settings@betweenSamples.min.class.size = 5
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128 settings@PeakPicking$fwhm = 6
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129 settings@PeakPicking$mzdiff = 0.5
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130 settings@betweenSamples.min.class.fraction = 0.5
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131 settings@betweenSamples.simthresh = 0.7
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132 settings@betweenSamples.rtdiff = 0.05
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133
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134
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135 #################
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136 # vary settings #
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137 #################
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138
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139 pop <- function(list) {
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140 # Removes the last item from a list.
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141 #
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142 # Args:
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143 # list: the list to pop.
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144 #
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145 # Returns:
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146 # The last item of the list before it was removed.
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147
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148 val <- list[length(list)]
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149 assign(as.character(substitute(list)), list[-length(list)], parent.frame())
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150 return (val)
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151
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152 }
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153
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154
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155 vary_list_to_settings <- function(settings, vary_list, title = "", titles_to_test = c(), settings_to_test = c()) {
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156 # Reads the list of parameters to vary and their ranges and builds a list of file titles and settings from it.
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157 #
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158 # Args:
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159 # settings: default settings for runGC.
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160 # vary_list: list of parameters to vary and the values each parameter must take.
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161 # title: title of the current file (concatenation of the values taken by the varied parameters).
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162 # titles_to_test: list of titles (one for each settings set) (concatenation of the values taken by the varied parameters).
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163 # settings_to_test: list of settings sets for runGC.
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164 #
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165 # Returns:
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166 # A list containing:
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167 # 1: the list of file titles ;
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168 # 2: the list of runGC() settings.
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169
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170 if (length(vary_list) == 0) { # if there are no parameters to vary
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171
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172 titles_to_test <- c(titles_to_test, "default_settings")
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173 settings_to_test <- c(settings_to_test, settings)
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174
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175 }
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176
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177 else {
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178
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179 param <- pop(vary_list)[[1]]
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180
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181 title <- paste0(title, param[1])
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182 setting <- param[2]
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183 range <- as.numeric(param[3:length(param)])
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184
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185 # for each possible value of the parameter
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186 for (p in range) {
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187
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188 # change the settings
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189 isSlot <- regexpr("\\$", setting)[1]
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190
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191 if (isSlot == -1) { # the parameter is a slot in class metaMSsettings
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192 slot(settings, setting) <- p
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193 }
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194 else { # the parameter is not a slot in class metaMSsettings
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195 slot(settings, substr(setting, 1, isSlot - 1))[substr(setting, isSlot + 1, nchar(setting))] <- p
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196 }
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197
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198 new_title <- paste0(title, "=", p, "_")
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199
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200 # save the settings in a list
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201 if (length(vary_list) == 0) {
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202 titles_to_test <- c(titles_to_test, new_title)
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203 settings_to_test <- c(settings_to_test, settings)
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204 }
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205 else {
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206 res <- vary_list_to_settings(settings, vary_list, new_title, titles_to_test, settings_to_test)
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207 titles_to_test <- res[[1]]
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208 settings_to_test <- res[[2]]
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209 }
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210
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211 } # end for
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212
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213 } # end else
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214
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215 return (list(titles_to_test, settings_to_test))
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216
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217 }
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218
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219
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220 ############
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221 # main #
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222 ############
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223
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224 # settings to vary and ranges of values
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225 res <- vary_list_to_settings(settings, vary_list)
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226 titles_to_test <- res[[1]]
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227 settings_to_test <- res[[2]]
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