int AbsoluteQuantitation::residualOutlierCandidate_(
const std::vector<AbsoluteQuantitationStandards::featureConcentration>& component_concentrations,
const String & feature_name,
const String & transformation_model,
const Param & transformation_model_params)
{
// Returns candidate outlier: A linear regression and residuals are calculated for
// the data points. The one with highest residual error is selected as the outlier candidate. The
// corresponding iterator position is then returned.
// fit the model
Param optimized_params = fitCalibration(component_concentrations,
feature_name,
transformation_model,
transformation_model_params);
// calculate the R2 and bias
std::vector<double> biases;
double correlation_coefficient = 0.0;
calculateBiasAndR(
component_concentrations,
feature_name,
transformation_model,
optimized_params,
biases,
correlation_coefficient);
return max_element(biases.begin(), biases.end()) - biases.begin();
}
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 << ".";
}
}
}
int AbsoluteQuantitation::jackknifeOutlierCandidate_(
const std::vector<AbsoluteQuantitationStandards::featureConcentration>& component_concentrations,
const String & feature_name,
const String & transformation_model,
const Param & transformation_model_params)
{
// Returns candidate outlier: A linear regression and rsq is calculated for
// the data points with one removed pair. The combination resulting in
// highest rsq is considered corresponding to the outlier candidate. The
// corresponding iterator position is then returned.
std::vector<double> rsq_tmp;
Param optimized_params = transformation_model_params;
for (Size i = 0; i < component_concentrations.size(); i++)
{
std::vector<AbsoluteQuantitationStandards::featureConcentration> component_concentrations_tmp = component_concentrations;
component_concentrations_tmp.erase(component_concentrations_tmp.begin() + i);
// debugging:
// std::cout << "jackknifeOutlierCandidate_: size of component_concentrations: " << std::to_string(component_concentrations_tmp.size()) << std::endl;
// fit the model
optimized_params = fitCalibration(component_concentrations_tmp,
feature_name,
transformation_model,
optimized_params);
// calculate the R2 and bias
std::vector<double> biases;
double correlation_coefficient = 0.0;
calculateBiasAndR(
component_concentrations_tmp,
feature_name,
transformation_model,
optimized_params,
biases,
correlation_coefficient);
rsq_tmp.push_back(correlation_coefficient);
}
return max_element(rsq_tmp.begin(), rsq_tmp.end()) - rsq_tmp.begin();
}
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 << ".";
}
}
}
bool AbsoluteQuantitation::optimizeCalibrationCurveIterative(
std::vector<AbsoluteQuantitationStandards::featureConcentration> & component_concentrations,
const String & feature_name,
const String & transformation_model,
const Param & transformation_model_params,
Param & optimized_params)
{
// sort from min to max concentration
std::vector<AbsoluteQuantitationStandards::featureConcentration> component_concentrations_sorted = component_concentrations;
std::sort(component_concentrations_sorted.begin(), component_concentrations_sorted.end(),
[](AbsoluteQuantitationStandards::featureConcentration lhs, AbsoluteQuantitationStandards::featureConcentration rhs)
{
return lhs.actual_concentration < rhs.actual_concentration; //ascending order
}
);
// indices of component_concentrations
std::vector<size_t> component_concentrations_sorted_indices;// loop from all points to min_points
for (size_t index = 0; index < component_concentrations_sorted.size(); ++index)
{
component_concentrations_sorted_indices.push_back(index);
}
// starting parameters
optimized_params = transformation_model_params;
// for (size_t n_iters = 0; n_iters < max_iters_; ++n_iters)
for (size_t n_iters = 0; n_iters < component_concentrations_sorted.size(); ++n_iters)
{
// extract out components
const std::vector<AbsoluteQuantitationStandards::featureConcentration> component_concentrations_sub = extractComponents_(
component_concentrations_sorted, component_concentrations_sorted_indices);
// check if the min number of calibration points has been broken
if (component_concentrations_sorted_indices.size() < min_points_)
{
LOG_INFO << "No optimal calibration found for " << component_concentrations_sub[0].feature.getMetaValue("native_id") << " .";
return false; //no optimal calibration found
}
// fit the model
optimized_params = fitCalibration(component_concentrations_sub,
feature_name,
transformation_model,
optimized_params);
// calculate the R2 and bias
std::vector<double> biases; // not needed (method parameters)
double correlation_coefficient = 0.0; // not needed (method parameters)
calculateBiasAndR(
component_concentrations_sub,
feature_name,
transformation_model,
optimized_params,
biases,
correlation_coefficient);
// check R2 and biases
bool bias_check = true;
for (size_t bias_it = 0; bias_it < biases.size(); ++bias_it)
{
if (biases[bias_it] > max_bias_)
{
bias_check = false;
}
}
if (bias_check && correlation_coefficient > min_correlation_coefficient_)
{
LOG_INFO << "Valid calibration found for " << component_concentrations_sub[0].feature.getMetaValue("native_id") << " .";
// copy over the final optimized points before exiting
component_concentrations = component_concentrations_sub;
return true; //optimal calibration found
}
// R2 and biases check failed, determine potential outlier
int pos;
if (outlier_detection_method_ == "iter_jackknife")
{
// get candidate outlier: removal of which datapoint results in best rsq?
pos = jackknifeOutlierCandidate_(
component_concentrations_sub,
feature_name,
transformation_model,
optimized_params);
}
else if (outlier_detection_method_ == "iter_residual")
{
// get candidate outlier: removal of datapoint with largest residual?
pos = residualOutlierCandidate_(
component_concentrations_sub,
feature_name,
transformation_model,
optimized_params);
}
else
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
String("Method ") + outlier_detection_method_ + " is not a valid method for optimizeCalibrationCurveIterative");
}
// remove if residual is an outlier according to Chauvenet's criterion
// or if testing is turned off
if (!use_chauvenet_ || MRMRTNormalizer::chauvenet(biases, pos))
{
component_concentrations_sorted_indices.erase(component_concentrations_sorted_indices.begin() + pos);
}
else
{
return false; //no optimal calibration found
}
}
return false; //no optimal calibration found
}
