| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | List of all members
MasstraceCorrelator Class Reference

Correlates individual masstraces found in mass spectrometric maps. More...

`#include <OpenMS/ANALYSIS/OPENSWATH/MasstraceCorrelator.h>`

Inheritance diagram for MasstraceCorrelator:

## Public Types

typedef std::vector< std::pair< double, double > > | MasstracePointsType
Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...

## Public Member Functions

| MasstraceCorrelator ()
| ~MasstraceCorrelator () override
void | createPseudoSpectra (const ConsensusMap &map, MSExperiment &pseudo_spectra, Size min_peak_nr, double min_correlation, int max_lag, double max_rt_apex_difference)
void | scoreHullpoints (const MasstracePointsType &hull_points1, const MasstracePointsType &hull_points2, int &lag, double &lag_intensity, double &pearson_score, const double min_corr, const int max_lag, const double mindiff=0.1)
void | createConsensusMapCache (const ConsensusMap &map, std::vector< MasstracePointsType > &feature_points, std::vector< std::pair< double, double > > &max_intensities, std::vector< double > &rt_cache)
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 &param)
| 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...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Protected Member Functions

void | matchMassTraces_ (const MasstracePointsType &hull_points1, const MasstracePointsType &hull_points2, std::vector< double > &vec1, std::vector< double > &vec2, double mindiff, double padEnds=true)
| Match up two mass traces with potentially missing values. More...
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...

## Additional Inherited Members

Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. 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...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

Correlates individual masstraces found in mass spectrometric maps.

The MasstraceCorrelator offers several functions to correlate individual mass traces using the normalized Cross-Correlation and pearson scoring of the OpenSWATH module.

## Member Typedef Documentation

## ◆ MasstracePointsType

typedef std::vector<std::pair<double, double> > MasstracePointsType

## Constructor & Destructor Documentation

## ◆ MasstraceCorrelator()

MasstraceCorrelator | ( |  | ) |

## ◆ ~MasstraceCorrelator()

~MasstraceCorrelator | ( |  | ) |

override

## Member Function Documentation

## ◆ createConsensusMapCache()

void createConsensusMapCache | ( | const ConsensusMap & | map,
|  | std::vector< MasstracePointsType > & | feature_points,
|  | std::vector< std::pair< double, double > > & | max_intensities,
|  | std::vector< double > & | rt_cache
| ) |  |

## ◆ createPseudoSpectra()

void createPseudoSpectra | ( | const ConsensusMap & | map,
|  | MSExperiment & | pseudo_spectra,
|  | Size | min_peak_nr,
|  | double | min_correlation,
|  | int | max_lag,
|  | double | max_rt_apex_difference
| ) |  |

Compute pseudo-spectra from a set of (MS2) masstraces

This function will take a set of masstraces (consensus map) as input and produce a vector of pseudo spectra as output (pseudo_spectra result vector).

It basically makes an all-vs-all comparison of all masstraces against each other and scores them on how similar they are in their mass traces.

This assumes that the consensus feature is only from one (SWATH) map This assumes that the consensus map is sorted by intensity

## ◆ matchMassTraces_()

void matchMassTraces_ | ( | const MasstracePointsType & | hull_points1,
|  | const MasstracePointsType & | hull_points2,
|  | std::vector< double > & | vec1,
|  | std::vector< double > & | vec2,
|  | double | mindiff,
|  | double | padEnds = `true`
| ) |  |

protected

Match up two mass traces with potentially missing values.

To compute correlations on masstraces, they need to have the same length and matching points. This function matches two masstraces by RT and identifies points that are the same in retention time (see mindiff parameter) and matches them. If no match is found, a missing value is assumed and they are filled with zeros. Thus, if the two retention times are less than mindiff apart, the two entries are considered to be equal, otherwise one is assumed to be zero).

This is useful for matching mass traces that are not of the exact same length and/or have missing values.

Parameters

  hull_points1 | The first input mass trace
  hull_points2 | The second input mass trace
  vec1 | The intensities of the first mass trace with matched-up points
  vec2 | The intensities of the second mass trace with matched-up points
  mindiff | The minimal difference in RT for points to match up
  padEnds | Whether to pad ends with zeros

## ◆ scoreHullpoints()

void scoreHullpoints | ( | const MasstracePointsType & | hull_points1,
|  | const MasstracePointsType & | hull_points2,
|  | int & | lag,
|  | double & | lag_intensity,
|  | double & | pearson_score,
|  | const double | min_corr,
|  | const int | max_lag,
|  | const double | mindiff = `0.1`
| ) |  |