void AbsoluteQuantitation::optimizeCalibrationCurves(
std::map<String, std::vector<AbsoluteQuantitationStandards::featureConcentration>> & components_concentrations)
{
for (auto& quant_method : quant_methods_)
{
// DEBUGGING
// std::cout << "optimizing calibration curves for " << quant_method.first << "." << std::endl;
if (components_concentrations.count(quant_method.first)>0 && optimization_method_ == "iterative")
{
// optimize the calibraiton curve for the component
Param optimized_params;
optimizeCalibrationCurveIterative(
components_concentrations[quant_method.first],
quant_method.second.getFeatureName(),
quant_method.second.getTransformationModel(),
quant_method.second.getTransformationModelParams(),
optimized_params);
// calculate the R2 and bias
std::vector<double> biases;
double correlation_coefficient = 0.0;
calculateBiasAndR(
components_concentrations[quant_method.first],
quant_method.second.getFeatureName(),
quant_method.second.getTransformationModel(),
optimized_params,
biases,
correlation_coefficient);
// record the updated information
quant_method.second.setCorrelationCoefficient(correlation_coefficient);
quant_method.second.setLLOQ(components_concentrations[quant_method.first][0].actual_concentration); //due to ascending sort
quant_method.second.setULOQ(components_concentrations[quant_method.first][components_concentrations[quant_method.first].size()-1].actual_concentration); //due to ascending sort
quant_method.second.setTransformationModelParams(optimized_params);
quant_method.second.setNPoints(components_concentrations[quant_method.first].size());
}
else if (optimization_method_ != "iterative")
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Unsupported calibration curve optimization method '" + optimization_method_ + "'.");
}
else
{
LOG_INFO << "Warning: Standards not found for component " << quant_method.first << ".";
}
}
}
void AbsoluteQuantitation::optimizeCalibrationCurves(
std::map<String, std::vector<AbsoluteQuantitationStandards::featureConcentration>> & components_concentrations)
{
std::map<String, std::vector<AbsoluteQuantitationStandards::featureConcentration>>& cc = components_concentrations;
for (std::pair<const String, AbsoluteQuantitationMethod>& quant_method : quant_methods_)
{
const String& component_name = quant_method.first;
AbsoluteQuantitationMethod& component_aqm = quant_method.second;
if (cc.count(component_name) && optimization_method_ == "iterative")
{
// optimize the calibration curve for the component
Param optimized_params;
bool optimal_calibration_found = optimizeCalibrationCurveIterative(
cc[component_name],
component_aqm.getFeatureName(),
component_aqm.getTransformationModel(),
component_aqm.getTransformationModelParams(),
optimized_params);
// order component concentrations and update the lloq and uloq
std::vector<AbsoluteQuantitationStandards::featureConcentration>::const_iterator it;
it = std::min_element(cc[component_name].begin(), cc[component_name].end(), [](
const AbsoluteQuantitationStandards::featureConcentration& lhs,
const AbsoluteQuantitationStandards::featureConcentration& rhs
)
{
return lhs.actual_concentration < rhs.actual_concentration;
}
);
component_aqm.setLLOQ(it->actual_concentration);
it = std::max_element(cc[component_name].begin(), cc[component_name].end(), [](
const AbsoluteQuantitationStandards::featureConcentration& lhs,
const AbsoluteQuantitationStandards::featureConcentration& rhs
)
{
return lhs.actual_concentration < rhs.actual_concentration;
}
);
component_aqm.setULOQ(it->actual_concentration);
if (optimal_calibration_found)
{
// calculate the R2 and bias
std::vector<double> biases;
double correlation_coefficient = 0.0;
calculateBiasAndR(
cc[component_name],
component_aqm.getFeatureName(),
component_aqm.getTransformationModel(),
optimized_params,
biases,
correlation_coefficient);
// record the updated information
component_aqm.setCorrelationCoefficient(correlation_coefficient);
component_aqm.setTransformationModelParams(optimized_params);
component_aqm.setNPoints(cc[component_name].size());
}
else
{
component_aqm.setCorrelationCoefficient(0.0);
component_aqm.setNPoints(0);
component_aqm.setLLOQ(0.0);
component_aqm.setULOQ(0.0);
}
}
else if (optimization_method_ != "iterative")
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Unsupported calibration curve optimization method '" + optimization_method_ + "'.");
}
else
{
LOG_DEBUG << "Warning: Standards not found for component " << component_name << ".";
}
}
}
