| OpenMS 2.5.0

Classes
OpenSwath::Scoring Namespace Reference

Scoring functions used by MRMScoring. More...

## Classes

struct | XCorrArrayType

## Typedefs

Type defs and helper structures
typedef std::pair< int, double > | XCorrEntry
| Cross Correlation array contains (lag,correlation) pairs. More...

## Functions

Helper functions
OPENSWATHALGO_DLLAPI double | NormalizedManhattanDist (double x[], double y[], int n)
| Calculate the normalized Manhattan distance between two arrays. More...
OPENSWATHALGO_DLLAPI double | RootMeanSquareDeviation (double x[], double y[], int n)
| Calculate the RMSD (root means square deviation) More...
OPENSWATHALGO_DLLAPI double | SpectralAngle (double x[], double y[], int n)
| Calculate the Spectral angle (acosine of the normalized dotproduct) More...
OPENSWATHALGO_DLLAPI XCorrArrayType | calcxcorr_legacy_mquest_ (std::vector< double > &data1, std::vector< double > &data2, bool normalize)
OPENSWATHALGO_DLLAPI XCorrArrayType | normalizedCrossCorrelation (std::vector< double > &data1, std::vector< double > &data2, const int &maxdelay, const int &lag)
OPENSWATHALGO_DLLAPI XCorrArrayType | calculateCrossCorrelation (const std::vector< double > &data1, const std::vector< double > &data2, const int &maxdelay, const int &lag)
| Calculate crosscorrelation on std::vector data without normalization. More...
OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator | xcorrArrayGetMaxPeak (const XCorrArrayType &array)
| Find best peak in an cross-correlation (highest apex) More...
OPENSWATHALGO_DLLAPI void | standardize_data (std::vector< double > &data)
| Standardize a vector (subtract mean, divide by standard deviation) More...
OPENSWATHALGO_DLLAPI void | normalize_sum (double x[], unsigned int n)
| divide each element of x by the sum of the vector More...
OPENSWATHALGO_DLLAPI std::vector< unsigned int > | computeRank (const std::vector< double > &w)
OPENSWATHALGO_DLLAPI double | rankedMutualInformation (std::vector< double > &data1, std::vector< double > &data2)

## Detailed Description

Scoring functions used by MRMScoring.

Many helper functions to calculate cross-correlations between data

## Typedef Documentation

## ◆ XCorrEntry

typedef std::pair<int, double> XCorrEntry

Cross Correlation array contains (lag,correlation) pairs.

## Function Documentation

## ◆ calculateCrossCorrelation()

OPENSWATHALGO_DLLAPI XCorrArrayType OpenSwath::Scoring::calculateCrossCorrelation | ( | const std::vector< double > & | data1,
|  | const std::vector< double > & | data2,
|  | const int & | maxdelay,
|  | const int & | lag
| ) |  |

Calculate crosscorrelation on std::vector data without normalization.

## ◆ calcxcorr_legacy_mquest_()

OPENSWATHALGO_DLLAPI XCorrArrayType OpenSwath::Scoring::calcxcorr_legacy_mquest_ | ( | std::vector< double > & | data1,
|  | std::vector< double > & | data2,
|  | bool | normalize
| ) |  |

Calculate crosscorrelation on std::vector data - Deprecated! Legacy code, this is a 1:1 port of the function from mQuest

## ◆ computeRank()

OPENSWATHALGO_DLLAPI std::vector<unsigned int> OpenSwath::Scoring::computeRank | ( | const std::vector< double > & | w | ) |

## ◆ normalize_sum()

OPENSWATHALGO_DLLAPI void OpenSwath::Scoring::normalize_sum | ( | double | x[],
|  | unsigned int | n
| ) |  |

divide each element of x by the sum of the vector

## ◆ normalizedCrossCorrelation()

OPENSWATHALGO_DLLAPI XCorrArrayType OpenSwath::Scoring::normalizedCrossCorrelation | ( | std::vector< double > & | data1,
|  | std::vector< double > & | data2,
|  | const int & | maxdelay,
|  | const int & | lag
| ) |  |

Calculate crosscorrelation on std::vector data (which is first normalized) NOTE: this replaces calcxcorr

Referenced by MRMTransitionGroupPicker::computeQuality_().

## ◆ NormalizedManhattanDist()

OPENSWATHALGO_DLLAPI double OpenSwath::Scoring::NormalizedManhattanDist | ( | double | x[],
|  | double | y[],
|  | int | n
| ) |  |

Calculate the normalized Manhattan distance between two arrays.

Equivalent to the function "delta_ratio_sum" from mQuest to calculate similarity between library intensity and experimental ones.

The delta_ratio_sum is calculated as follows:

## ◆ rankedMutualInformation()

OPENSWATHALGO_DLLAPI double OpenSwath::Scoring::rankedMutualInformation | ( | std::vector< double > & | data1,
|  | std::vector< double > & | data2
| ) |  |

Referenced by MRMTransitionGroupPicker::pickFragmentChromatograms().

## ◆ RootMeanSquareDeviation()

OPENSWATHALGO_DLLAPI double OpenSwath::Scoring::RootMeanSquareDeviation | ( | double | x[],
|  | double | y[],
|  | int | n
| ) |  |

Calculate the RMSD (root means square deviation)

The RMSD is calculated as follows:

## ◆ SpectralAngle()

OPENSWATHALGO_DLLAPI double OpenSwath::Scoring::SpectralAngle | ( | double | x[],
|  | double | y[],
|  | int | n
| ) |  |

Calculate the Spectral angle (acosine of the normalized dotproduct)

The spectral angle is calculated as follows:

## ◆ standardize_data()

OPENSWATHALGO_DLLAPI void OpenSwath::Scoring::standardize_data | ( | std::vector< double > & | data | ) |

Standardize a vector (subtract mean, divide by standard deviation)

## ◆ xcorrArrayGetMaxPeak()

OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator OpenSwath::Scoring::xcorrArrayGetMaxPeak | ( | const XCorrArrayType & | array | ) |

Find best peak in an cross-correlation (highest apex)

Referenced by MRMTransitionGroupPicker::computeQuality_().