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OpenMS
2.4.0
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Scoring functions used by MRMScoring. More...
Classes | |
struct | XCorrArrayType |
Scoring functions used by MRMScoring.
Many helper functions to calculate cross-correlations between data
typedef std::pair<int, double> XCorrEntry |
Cross Correlation array contains (lag,correlation) pairs.
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.
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
OPENSWATHALGO_DLLAPI std::vector<unsigned int> OpenSwath::Scoring::computeRank | ( | const std::vector< double > & | w | ) |
OPENSWATHALGO_DLLAPI void OpenSwath::Scoring::normalize_sum | ( | double | x[], |
unsigned int | n | ||
) |
divide each element of x by the sum of the vector
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_().
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:
OPENSWATHALGO_DLLAPI double OpenSwath::Scoring::rankedMutualInformation | ( | std::vector< double > & | data1, |
std::vector< double > & | data2 | ||
) |
Referenced by MRMTransitionGroupPicker::createMRMFeature().
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:
Calculate the Spectral angle (acosine of the normalized dotproduct)
The spectral angle is calculated as follows:
OPENSWATHALGO_DLLAPI void OpenSwath::Scoring::standardize_data | ( | std::vector< double > & | data | ) |
Standardize a vector (subtract mean, divide by standard deviation)
OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator OpenSwath::Scoring::xcorrArrayGetMaxPeak | ( | const XCorrArrayType & | array | ) |
Find best peak in an cross-correlation (highest apex)
Referenced by MRMTransitionGroupPicker::computeQuality_().