Implementation of the Ascore For a given peptide sequence and its MS^2 spectrum it is tried to identify the most probable phosphorylation-site(s). For each phosphorylation site a score is calculated, which is an indicator for the probability that this site is phosphorylated. The algorithm is implemented according to Beausoleil et al. More...
#include <OpenMS/ANALYSIS/ID/AScore.h>
Public Member Functions | |
| AScore () | |
| Default constructor. More... | |
| ~AScore () | |
| Destructor. More... | |
| PeptideHit | compute (PeptideHit &hit, RichPeakSpectrum &real_spectrum, DoubleReal fmt, Int number_of_phospho_sites) |
| Computes the AScore and returns all computed phospho-sites. The saved sequences contain only phospho informations. All other modifications are dropped due to simplicity. More... | |
| DoubleReal | computeCumulativeScore (UInt N, UInt n, DoubleReal p) |
| Computes the cumulative binomial probabilities. More... | |
| void | computeHighestPeptides (std::vector< std::vector< DoubleReal > > &peptide_site_scores, std::vector< ProbablePhosphoSites > &sites, std::vector< std::vector< Size > > &permutations) |
| Finds the peptides with the highest PeptideScores and outputs all informations for computing the AScore. More... | |
| void | compute_site_determining_ions (std::vector< RichPeakSpectrum > &th_spectra, ProbablePhosphoSites &candidates, Int charge, std::vector< RichPeakSpectrum > &site_determining_ions) |
| Computes the site determining_ions for the given AS and sequences in candidates. More... | |
| std::vector< Size > | computeTupel_ (AASequence &without_phospho) |
| helperfunction More... | |
| std::vector< std::vector< Size > > | computePermutations_ (std::vector< Size > tupel, Int number_of_phospho_sites) |
| helper function More... | |
Private Member Functions | |
| Int | numberOfMatchedIons_ (const RichPeakSpectrum &th, const RichPeakSpectrum &windows, Size depth, DoubleReal fmt) |
| computes number of matched ions between windows and the given spectrum. All spectra have to be sorted by Position! More... | |
| DoubleReal | peptideScore_ (std::vector< DoubleReal > &scores) |
| computes the peptide score according to Beausoleil et al. page 1291 More... | |
Implementation of the Ascore For a given peptide sequence and its MS^2 spectrum it is tried to identify the most probable phosphorylation-site(s). For each phosphorylation site a score is calculated, which is an indicator for the probability that this site is phosphorylated. The algorithm is implemented according to Beausoleil et al.
| AScore | ( | ) |
Default constructor.
| ~AScore | ( | ) |
Destructor.
| PeptideHit compute | ( | PeptideHit & | hit, |
| RichPeakSpectrum & | real_spectrum, | ||
| DoubleReal | fmt, | ||
| Int | number_of_phospho_sites | ||
| ) |
Computes the AScore and returns all computed phospho-sites. The saved sequences contain only phospho informations. All other modifications are dropped due to simplicity.
| hit | a PeptideHit |
| real_spectrum | spectrum mapped to hit |
| fmt | fragment_mass_tolerance, when comparing real_spectrum to a theoretical spectrum of the amino acid sequence of hit. |
| number_of_phospho_sites | which directs the method to search for this number of phosphorylated sites. |
| void compute_site_determining_ions | ( | std::vector< RichPeakSpectrum > & | th_spectra, |
| ProbablePhosphoSites & | candidates, | ||
| Int | charge, | ||
| std::vector< RichPeakSpectrum > & | site_determining_ions | ||
| ) |
Computes the site determining_ions for the given AS and sequences in candidates.
| DoubleReal computeCumulativeScore | ( | UInt | N, |
| UInt | n, | ||
| DoubleReal | p | ||
| ) |
Computes the cumulative binomial probabilities.
| void computeHighestPeptides | ( | std::vector< std::vector< DoubleReal > > & | peptide_site_scores, |
| std::vector< ProbablePhosphoSites > & | sites, | ||
| std::vector< std::vector< Size > > & | permutations | ||
| ) |
Finds the peptides with the highest PeptideScores and outputs all informations for computing the AScore.
| std::vector<std::vector<Size> > computePermutations_ | ( | std::vector< Size > | tupel, |
| Int | number_of_phospho_sites | ||
| ) |
helper function
| std::vector<Size> computeTupel_ | ( | AASequence & | without_phospho | ) |
helperfunction
|
private |
computes number of matched ions between windows and the given spectrum. All spectra have to be sorted by Position!
|
private |
computes the peptide score according to Beausoleil et al. page 1291
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |