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 |