Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture. More...
#include <OpenMS/MATH/STATISTICS/PosteriorErrorProbabilityModel.h>
 
  
 | Public Member Functions | |
| PosteriorErrorProbabilityModel () | |
| default constructor  More... | |
| virtual | ~PosteriorErrorProbabilityModel () | 
| Destructor.  More... | |
| bool | fit (std::vector< double > &search_engine_scores) | 
| fits the distributions to the data points(search_engine_scores). Estimated parameters for the distributions are saved in member variables. computeProbability can be used afterwards.  More... | |
| bool | fit (std::vector< double > &search_engine_scores, std::vector< double > &probabilities) | 
| fits the distributions to the data points(search_engine_scores) and writes the computed probabilites into the given vector (the second one).  More... | |
| void | fillDensities (std::vector< double > &x_scores, std::vector< DoubleReal > &incorrect_density, std::vector< DoubleReal > &correct_density) | 
| Writes the distributions densities into the two vectors for a set of scores. Incorrect_densities represent the incorreclty assigned seqeuences.  More... | |
| DoubleReal | computeMaxLikelihood (std::vector< DoubleReal > &incorrect_density, std::vector< DoubleReal > &correct_density) | 
| computes the Maximum Likelihood with a log-likelihood funciotn.  More... | |
| DoubleReal | one_minus_sum_post (std::vector< DoubleReal > &incorrect_density, std::vector< DoubleReal > &correct_density) | 
| sums (1 - posterior porbabilities)  More... | |
| DoubleReal | sum_post (std::vector< DoubleReal > &incorrect_density, std::vector< DoubleReal > &correct_density) | 
| sums posterior porbabilities  More... | |
| DoubleReal | sum_pos_x0 (std::vector< double > &x_scores, std::vector< DoubleReal > &incorrect_density, std::vector< DoubleReal > &correct_density) | 
| helper function for the EM algorithm (for fitting)  More... | |
| DoubleReal | sum_neg_x0 (std::vector< double > &x_scores, std::vector< DoubleReal > &incorrect_density, std::vector< DoubleReal > &correct_density) | 
| helper function for the EM algorithm (for fitting)  More... | |
| DoubleReal | sum_pos_sigma (std::vector< double > &x_scores, std::vector< DoubleReal > &incorrect_density, std::vector< DoubleReal > &correct_density, DoubleReal positive_mean) | 
| helper function for the EM algorithm (for fitting)  More... | |
| DoubleReal | sum_neg_sigma (std::vector< double > &x_scores, std::vector< DoubleReal > &incorrect_density, std::vector< DoubleReal > &correct_density, DoubleReal positive_mean) | 
| helper function for the EM algorithm (for fitting)  More... | |
| GaussFitter::GaussFitResult | getCorrectlyAssignedFitResult () const | 
| returns estimated parameters for correctly assigned sequences. Fit should be used before.  More... | |
| GaussFitter::GaussFitResult | getIncorrectlyAssignedFitResult () const | 
| returns estimated parameters for correctly assigned sequences. Fit should be used before.  More... | |
| DoubleReal | getNegativePrior () const | 
| returns the estimated negative prior probability.  More... | |
| DoubleReal | getGauss (DoubleReal x, const GaussFitter::GaussFitResult ¶ms) | 
| computes the gaussian density at position x with parameters params.  More... | |
| DoubleReal | getGumbel (DoubleReal x, const GaussFitter::GaussFitResult ¶ms) | 
| computes the gumbel density at position x with parameters params.  More... | |
| DoubleReal | computeProbability (DoubleReal score) | 
| TextFile * | InitPlots (std::vector< double > &x_scores) | 
| initializes the plots  More... | |
| const String | getGumbelGnuplotFormula (const GaussFitter::GaussFitResult ¶ms) const | 
| returns the gnuplot formula of the fitted gumbel distribution. Only x0 and sigma are used as local parameter alpha and scale parameter beta, respectively.  More... | |
| const String | getGaussGnuplotFormula (const GaussFitter::GaussFitResult ¶ms) const | 
| returns the gnuplot formula of the fitted gauss distribution.  More... | |
| const String | getBothGnuplotFormula (const GaussFitter::GaussFitResult &incorrect, const GaussFitter::GaussFitResult &correct) const | 
| returns the gnuplot formula of the fitted mixture distribution.  More... | |
| void | plotTargetDecoyEstimation (std::vector< double > &target, std::vector< double > &decoy) | 
| plots the estimated distribution against target and decoy hits  More... | |
| DoubleReal | getSmallestScore () | 
| returns the smallest score used in the last fit  More... | |
|  Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages.  More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor.  More... | |
| virtual | ~DefaultParamHandler () | 
| Destructor.  More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
| Private Member Functions | |
| PosteriorErrorProbabilityModel & | operator= (const PosteriorErrorProbabilityModel &rhs) | 
| assignment operator (not implemented)  More... | |
| PosteriorErrorProbabilityModel (const PosteriorErrorProbabilityModel &rhs) | |
| Copy constructor (not implemented)  More... | |
| Private Attributes | |
| GaussFitter::GaussFitResult | incorrectly_assigned_fit_param_ | 
| stores parameters for incorrectly assigned sequences. If gumbel fit was used, A can be ignored. Furthermore, in this case, x0 and sigma are the local parameter alpha and scale parameter beta, respectively.  More... | |
| GaussFitter::GaussFitResult | correctly_assigned_fit_param_ | 
| stores gauss parameters  More... | |
| DoubleReal | negative_prior_ | 
| stores final prior probability for negative peptides  More... | |
| DoubleReal | max_incorrectly_ | 
| peak of the incorrectly assigned sequences distribution  More... | |
| DoubleReal | max_correctly_ | 
| peak of the gauss distribution (correctly assigned sequences)  More... | |
| DoubleReal | smallest_score_ | 
| smallest score which was used for fitting the model  More... | |
| DoubleReal(PosteriorErrorProbabilityModel::* | calc_incorrect_ )(DoubleReal x, const GaussFitter::GaussFitResult ¶ms) | 
| points to getGauss  More... | |
| DoubleReal(PosteriorErrorProbabilityModel::* | calc_correct_ )(DoubleReal x, const GaussFitter::GaussFitResult ¶ms) | 
| points either to getGumbel or getGauss depending on whether on uses the gumbel or th gausian distribution for incorrectly assigned sequences.  More... | |
| const String(PosteriorErrorProbabilityModel::* | getNegativeGnuplotFormula_ )(const GaussFitter::GaussFitResult ¶ms) const | 
| points either to getGumbelGnuplotFormula or getGaussGnuplotFormula depending on whether on uses the gumbel or th gausian distribution for incorrectly assigned sequences.  More... | |
| const String(PosteriorErrorProbabilityModel::* | getPositiveGnuplotFormula_ )(const GaussFitter::GaussFitResult ¶ms) const | 
| points to getGumbelGnuplotFormula  More... | |
| Additional Inherited Members | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| virtual void | updateMembers_ () | 
| This method is used to update extra member variables at the end of the setParameters() method.  More... | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
|  Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ | 
| Container for current parameters.  More... | |
| Param | defaults_ | 
| Container for default parameters. This member should be filled in the constructor of derived classes!  More... | |
| std::vector< String > | subsections_ | 
| Container for registered subsections. This member should be filled in the constructor of derived classes!  More... | |
| String | error_name_ | 
| Name that is displayed in error messages during the parameter checking.  More... | |
| bool | check_defaults_ | 
| If this member is set to false no checking if parameters in done;.  More... | |
| bool | warn_empty_defaults_ | 
| If this member is set to false no warning is emitted when defaults are empty;.  More... | |
Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture.
This class fits either a Gumbel distribution and a Gauss distribution to a set of data points or two Gaussian distributions using the EM algorithm. One can output the fit as a gnuplot formula using getGumbelGnuplotFormula() and getGaussGnuplotFormula() after fitting.
| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| number_of_bins | int | 100 | Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized | |
| output_plots | string | false | true, false | If true every step of the EM-algorithm will be written to a file as a gnuplot formula | 
| output_name | string | If output_plots is on, the output files will be saved in the following manner: | ||
| incorrectly_assigned | string | Gumbel | Gumbel, Gauss | for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used. | 
default constructor
| 
 | virtual | 
Destructor.
| 
 | private | 
Copy constructor (not implemented)
| DoubleReal computeMaxLikelihood | ( | std::vector< DoubleReal > & | incorrect_density, | 
| std::vector< DoubleReal > & | correct_density | ||
| ) | 
computes the Maximum Likelihood with a log-likelihood funciotn.
| DoubleReal computeProbability | ( | DoubleReal | score | ) | 
Returns the computed posterior error probability for a given score.
| void fillDensities | ( | std::vector< double > & | x_scores, | 
| std::vector< DoubleReal > & | incorrect_density, | ||
| std::vector< DoubleReal > & | correct_density | ||
| ) | 
Writes the distributions densities into the two vectors for a set of scores. Incorrect_densities represent the incorreclty assigned seqeuences.
| bool fit | ( | std::vector< double > & | search_engine_scores | ) | 
fits the distributions to the data points(search_engine_scores). Estimated parameters for the distributions are saved in member variables. computeProbability can be used afterwards.
| search_engine_scores | a vector which holds the data points | 
fits the distributions to the data points(search_engine_scores) and writes the computed probabilites into the given vector (the second one).
| search_engine_scores | a vector which holds the data points | 
| probabilities | a vector which holds the probability for each data point after running this function. If it has some content it will be overwritten. | 
| const String getBothGnuplotFormula | ( | const GaussFitter::GaussFitResult & | incorrect, | 
| const GaussFitter::GaussFitResult & | correct | ||
| ) | const | 
returns the gnuplot formula of the fitted mixture distribution.
| 
 | inline | 
returns estimated parameters for correctly assigned sequences. Fit should be used before.
| 
 | inline | 
computes the gaussian density at position x with parameters params.
References GaussFitter::GaussFitResult::A, GaussFitter::GaussFitResult::sigma, and GaussFitter::GaussFitResult::x0.
| const String getGaussGnuplotFormula | ( | const GaussFitter::GaussFitResult & | params | ) | const | 
returns the gnuplot formula of the fitted gauss distribution.
| 
 | inline | 
computes the gumbel density at position x with parameters params.
References GaussFitter::GaussFitResult::sigma, and GaussFitter::GaussFitResult::x0.
| const String getGumbelGnuplotFormula | ( | const GaussFitter::GaussFitResult & | params | ) | const | 
returns the gnuplot formula of the fitted gumbel distribution. Only x0 and sigma are used as local parameter alpha and scale parameter beta, respectively.
| 
 | inline | 
returns estimated parameters for correctly assigned sequences. Fit should be used before.
| 
 | inline | 
returns the estimated negative prior probability.
| 
 | inline | 
returns the smallest score used in the last fit
| DoubleReal one_minus_sum_post | ( | std::vector< DoubleReal > & | incorrect_density, | 
| std::vector< DoubleReal > & | correct_density | ||
| ) | 
sums (1 - posterior porbabilities)
| 
 | private | 
assignment operator (not implemented)
plots the estimated distribution against target and decoy hits
| DoubleReal sum_neg_sigma | ( | std::vector< double > & | x_scores, | 
| std::vector< DoubleReal > & | incorrect_density, | ||
| std::vector< DoubleReal > & | correct_density, | ||
| DoubleReal | positive_mean | ||
| ) | 
helper function for the EM algorithm (for fitting)
| DoubleReal sum_neg_x0 | ( | std::vector< double > & | x_scores, | 
| std::vector< DoubleReal > & | incorrect_density, | ||
| std::vector< DoubleReal > & | correct_density | ||
| ) | 
helper function for the EM algorithm (for fitting)
| DoubleReal sum_pos_sigma | ( | std::vector< double > & | x_scores, | 
| std::vector< DoubleReal > & | incorrect_density, | ||
| std::vector< DoubleReal > & | correct_density, | ||
| DoubleReal | positive_mean | ||
| ) | 
helper function for the EM algorithm (for fitting)
| DoubleReal sum_pos_x0 | ( | std::vector< double > & | x_scores, | 
| std::vector< DoubleReal > & | incorrect_density, | ||
| std::vector< DoubleReal > & | correct_density | ||
| ) | 
helper function for the EM algorithm (for fitting)
| DoubleReal sum_post | ( | std::vector< DoubleReal > & | incorrect_density, | 
| std::vector< DoubleReal > & | correct_density | ||
| ) | 
sums posterior porbabilities
| 
 | private | 
points either to getGumbel or getGauss depending on whether on uses the gumbel or th gausian distribution for incorrectly assigned sequences.
| 
 | private | 
points to getGauss
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 | private | 
stores gauss parameters
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 | private | 
points either to getGumbelGnuplotFormula or getGaussGnuplotFormula depending on whether on uses the gumbel or th gausian distribution for incorrectly assigned sequences.
| 
 | private | 
points to getGumbelGnuplotFormula
| 
 | private | 
stores parameters for incorrectly assigned sequences. If gumbel fit was used, A can be ignored. Furthermore, in this case, x0 and sigma are the local parameter alpha and scale parameter beta, respectively.
| 
 | private | 
peak of the gauss distribution (correctly assigned sequences)
| 
 | private | 
peak of the incorrectly assigned sequences distribution
| 
 | private | 
stores final prior probability for negative peptides
| 
 | private | 
smallest score which was used for fitting the model
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:38 using doxygen 1.8.5 |