| OpenMS 2.5.0

AbsoluteQuantitation.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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31 // $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
32 // $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/config.h>
38
39 //Kernal classes
40 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
41 #include <OpenMS/KERNEL/StandardTypes.h>
42 #include <OpenMS/KERNEL/MSExperiment.h>
43 #include <OpenMS/KERNEL/MSChromatogram.h>
44 #include <OpenMS/KERNEL/FeatureMap.h>
45 #include <OpenMS/KERNEL/MRMTransitionGroup.h>
46 #include <OpenMS/KERNEL/MRMFeature.h>
47
48 //Analysis classes
49 #include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
50 #include <OpenMS/ANALYSIS/MAPMATCHING/TransformationModel.h>
51 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
52
53 //Quantitation classes
54 #include <OpenMS/METADATA/AbsoluteQuantitationStandards.h>
55 #include <OpenMS/ANALYSIS/QUANTITATION/AbsoluteQuantitationMethod.h>
56
57
58 //Standard library
59 #include <cstddef> // for size_t & ptrdiff_t
60 #include <vector>
61 #include <string>
62
63 namespace OpenMS
64 {
65
84 class OPENMS_DLLAPI AbsoluteQuantitation :
85 public DefaultParamHandler
86 {
87
88 public:
90 AbsoluteQuantitation();
92
94 ~AbsoluteQuantitation();
96
103 void setQuantMethods(std::vector<AbsoluteQuantitationMethod>& quant_methods);
104
105
109 std::vector<AbsoluteQuantitationMethod> getQuantMethods();
110 std::map<String, AbsoluteQuantitationMethod> getQuantMethodsAsMap();
111
124 double calculateRatio(const Feature & component_1, const Feature & component_2, const String & feature_name);
125
142 double calculateBias(const double & actual_concentration, const double & calculated_concentration);
143
156 Param fitCalibration(const std::vector<AbsoluteQuantitationStandards::featureConcentration> & component_concentrations,
157 const String & feature_name,
158 const String & transformation_model,
159 const Param & transformation_model_params);
160
173 void calculateBiasAndR(
174 const std::vector<AbsoluteQuantitationStandards::featureConcentration> & component_concentrations,
175 const String & feature_name,
176 const String & transformation_model,
177 const Param & transformation_model_params,
178 std::vector<double> & biases,
179 double & correlation_coefficient);
180
196 bool optimizeCalibrationCurveIterative(
197 std::vector<AbsoluteQuantitationStandards::featureConcentration> & component_concentrations,
198 const String & feature_name,
199 const String & transformation_model,
200 const Param & transformation_model_params,
201 Param & optimized_params);
202
212 void optimizeCalibrationCurves(std::map<String,std::vector<AbsoluteQuantitationStandards::featureConcentration>> & components_concentrations);
213
223 void optimizeSingleCalibrationCurve(
224 const String& component_name,
225 std::vector<AbsoluteQuantitationStandards::featureConcentration>& component_concentrations
226 );
227
242 double applyCalibration(const Feature & component,
243 const Feature & IS_component,
244 const String & feature_name,
245 const String & transformation_model,
246 const Param & transformation_model_params);
247
261 void quantifyComponents(FeatureMap& unknowns);
262
263 protected:
274 std::vector<AbsoluteQuantitationStandards::featureConcentration> extractComponents_(
275 const std::vector<AbsoluteQuantitationStandards::featureConcentration> & component_concentrations,
276 const std::vector<size_t>& component_concentrations_indices);
277
292 int jackknifeOutlierCandidate_(
293 const std::vector<AbsoluteQuantitationStandards::featureConcentration>& component_concentrations,
294 const String & feature_name,
295 const String & transformation_model,
296 const Param & transformation_model_params);
297
312 int residualOutlierCandidate_(
313 const std::vector<AbsoluteQuantitationStandards::featureConcentration>& component_concentrations,
314 const String & feature_name,
315 const String & transformation_model,
316 const Param & transformation_model_params);
317
318 private:
320 void updateMembers_();
321
322 size_t min_points_;
323 double max_bias_;
324 double min_correlation_coefficient_;
325 size_t max_iters_;
326 String outlier_detection_method_;
327 bool use_chauvenet_;
328 String optimization_method_;
329
330 // members
332 std::map<String, AbsoluteQuantitationMethod> quant_methods_;
333
334 };
335
336 }
337
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::AbsoluteQuantitation::quant_methods_
std::map< String, AbsoluteQuantitationMethod > quant_methods_
map between components and quantitation methods
Definition: AbsoluteQuantitation.h:332
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::AbsoluteQuantitation::max_bias_
double max_bias_
Definition: AbsoluteQuantitation.h:323
OpenMS::AbsoluteQuantitation::min_points_
size_t min_points_
Definition: AbsoluteQuantitation.h:322
TargetedExperiment.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
StandardTypes.h
FeatureMap.h
OpenMS::AbsoluteQuantitation
AbsoluteQuantitation is a class to support absolute or relative quantitation for targeted or untarget...
Definition: AbsoluteQuantitation.h:84
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::AbsoluteQuantitation::optimization_method_
String optimization_method_
Definition: AbsoluteQuantitation.h:328
TransformationDescription.h
DefaultParamHandler.h
OpenMS::AbsoluteQuantitation::min_correlation_coefficient_
double min_correlation_coefficient_
Definition: AbsoluteQuantitation.h:324
OpenMS::AbsoluteQuantitation::use_chauvenet_
bool use_chauvenet_
Definition: AbsoluteQuantitation.h:327
TransformationModel.h
MRMFeature.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::AbsoluteQuantitation::max_iters_
size_t max_iters_
Definition: AbsoluteQuantitation.h:325
OpenMS::AbsoluteQuantitation::outlier_detection_method_
String outlier_detection_method_
Definition: AbsoluteQuantitation.h:326
AbsoluteQuantitationStandards.h
MSChromatogram.h
AbsoluteQuantitationMethod.h
MRMTransitionGroup.h