FragmentIonLikelihoodModel.h File Reference

#include <OpenMS/CHEMISTRY/Residue.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Macros.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <cstdint>
#include <string>
#include <vector>

Go to the source code of this file.

Classes
class	FragmentIonLikelihoodModel
	Per-run likelihood model of fragment ion presence, intensity rank and mass error, learned from confident PSMs. More...
class	FragmentIonLikelihoodModel::PeakLists
	Compact peak lists of the spectra of one run: per peak only its m/z and its intensity-rank bin. More...
struct	FragmentIonLikelihoodModel::Ion
	One theoretical ion after matching. More...
struct	FragmentIonLikelihoodModel::Features
	Features of one PSM. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::FragmentIonLikelihoodModel::Ion

struct OpenMS::FragmentIonLikelihoodModel::Ion

One theoretical ion after matching.

Class Members
UInt32	context	flat context index, below contexts()
UInt32	outcome	outcome index, below outcomes(); absentOutcome() if unmatched

OpenMS::FragmentIonLikelihoodModel::Features

struct OpenMS::FragmentIonLikelihoodModel::Features

Features of one PSM.

Class Members
double	explained_presence = 0.0	sum of P(present) over matched ions / sum of P(present) over all ions
double	log_likelihood_ratio = 0.0	sum over all theoretical ions of ln P(outcome | signal) / P(outcome | noise)
Size	matched_ions = 0	theoretical ions with a peak within tolerance
Size	theoretical_ions = 0	theoretical ions with a recognised ion name
double	top_predicted_observed = 0.0	fraction of the top_k ions with the highest P(present) that matched