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OpenMS
2.5.0
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38 #include <boost/math/special_functions/fpclassify.hpp>
79 template<
typename SpectrumType,
class TransitionT>
82 std::vector<double> fit_scores;
84 bool smooth_data =
false;
94 fit_scores.push_back(fscore);
98 avg_score /= transition_group.
size();
107 if (current_section.size() < 2)
114 typedef Peak1D LocalPeakType;
117 std::vector<LocalPeakType> data_to_fit;
118 prepareFit_(current_section, data_to_fit, smooth_data);
120 double quality =
fitRT_(data_to_fit, model_rt);
129 template<
class LocalPeakType>
151 if (boost::math::isnan(quality)) quality = -1.0;
157 template<
class LocalPeakType>
163 for (ConvexHull2D::PointArrayType::const_iterator it = current_section.begin(); it != current_section.end(); it++)
167 p.setIntensity(it->getY());
168 filter_spec.push_back(p);
173 std::vector<double> distances;
174 for (
Size j = 1; j < filter_spec.size(); ++j)
176 distances.push_back(filter_spec[j].getMZ() - filter_spec[j - 1].getMZ());
178 double dist_average = std::accumulate(distances.begin(), distances.end(), 0.0) / (
double) distances.size();
183 new_peak.
setMZ(filter_spec.back().getMZ() + dist_average);
184 filter_spec.push_back(new_peak);
185 new_peak.
setMZ(filter_spec.back().getMZ() + dist_average);
186 filter_spec.push_back(new_peak);
187 new_peak.
setMZ(filter_spec.back().getMZ() + dist_average);
188 filter_spec.push_back(new_peak);
191 new_peak.
setMZ(filter_spec.front().getMZ() - dist_average);
192 filter_spec.insert(filter_spec.begin(), new_peak);
193 new_peak.
setMZ(filter_spec.front().getMZ() - dist_average);
194 filter_spec.insert(filter_spec.begin(), new_peak);
195 new_peak.
setMZ(filter_spec.front().getMZ() - dist_average);
196 filter_spec.insert(filter_spec.begin(), new_peak);
205 filter_param.setValue(
"gaussian_width", 4 * dist_average);
207 filter.
filter(filter_spec);
211 for (
Size j = 0; j != filter_spec.size(); ++j)
214 p.setPosition(filter_spec[j].getMZ());
215 p.setIntensity(filter_spec[j].getIntensity());
216 data_to_fit.push_back(p);
const std::vector< ConvexHull2D > & getConvexHulls() const
Non-mutable access to the convex hulls.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
A more convenient string class.
Definition: String.h:58
void filter(MSSpectrum &spectrum)
Smoothes an MSSpectrum containing profile data.
Definition: GaussFilter.h:92
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
~EmgScoring()
Definition: EmgScoring.h:66
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: openms/include/OpenMS/CONCEPT/Macros.h:136
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
std::vector< PointType > PointArrayType
Definition: ConvexHull2D.h:76
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Feature & getFeature(const String &key)
get a specified feature
void setFitterParam(Param param)
Definition: EmgScoring.h:68
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:54
Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eig...
Definition: EmgFitter1D.h:46
void prepareFit_(const ConvexHull2D::PointArrayType ¤t_section, std::vector< LocalPeakType > &data_to_fit, bool smooth_data)
Definition: EmgScoring.h:158
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
const Param & getParameters() const
Non-mutable access to the parameters.
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
double fitRT_(std::vector< LocalPeakType > &rt_input_data, InterpolationModel *&model)
Definition: EmgScoring.h:130
double elutionModelFit(ConvexHull2D::PointArrayType current_section, bool smooth_data)
Definition: EmgScoring.h:104
Scoring of an elution peak using an exponentially modified gaussian distribution model.
Definition: EmgScoring.h:59
An LC-MS feature.
Definition: Feature.h:70
EmgScoring()
Definition: EmgScoring.h:64
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:67
QualityType fit1d(const RawDataArrayType &range, InterpolationModel *&model) override
return interpolation model
Management and storage of parameters / INI files.
Definition: Param.h:73
Param getDefaults()
Definition: EmgScoring.h:73
std::vector< ChromatogramType > & getChromatograms()
Definition: MRMTransitionGroup.h:174
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
double calcElutionFitScore(MRMFeature &mrmfeature, MRMTransitionGroup< SpectrumType, TransitionT > &transition_group)
calculate the elution profile fit score
Definition: EmgScoring.h:80
Size size() const
Definition: MRMTransitionGroup.h:125
This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...
Definition: GaussFilter.h:74
EmgFitter1D fitter_emg1D_
Definition: EmgScoring.h:220