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IDFilter Class Reference

#include <OpenMS/FILTERING/ID/IDFilter.h>

List of all members.


Detailed Description

used to filter identifications by different criteria

The identifications are filtered by significance thresholds and by sequences. The filtering by significance thresholds looks for the best ProteinIdentification that fullfills the significance threshold criterium. score > significance-threshold * significance_fraction. The filtering by sequences looks for the best ProteinIdentification that is contained in one of the protein sequences.

Public Member Functions

 IDFilter ()
 Constructor.
 ~IDFilter ()
 Destructor.
template<class IdentificationType>
void filterIdentificationsByThreshold (const IdentificationType &identification, DoubleReal threshold_fraction, IdentificationType &filtered_identification)
 filters a ProteinIdentification or PeptideIdentification corresponding to the threshold_fraction
template<class IdentificationType>
void filterIdentificationsByScore (const IdentificationType &identification, DoubleReal threshold_score, IdentificationType &filtered_identification)
 filters a ProteinIdentification or PeptideIdentification corresponding to the threshold_score
template<class IdentificationType>
void filterIdentificationsByBestNHits (const IdentificationType &identification, UInt n, IdentificationType &filtered_identification)
 filters a ProteinIdentification or PeptideIdentification corresponding to the score.
void filterIdentificationsByBestHits (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, bool strict=false)
 filters a PeptideIdentification keeping only the best scoring hits (if strict is set, keeping only the best hit only if it is the only hit with that score)
void filterIdentificationsByProteins (const PeptideIdentification &identification, std::vector< std::pair< String, String > > proteins, PeptideIdentification &filtered_identification)
 filters a PeptideIdentification corresponding to the given proteins
void filterIdentificationsByProteins (const ProteinIdentification &identification, std::vector< std::pair< String, String > > proteins, ProteinIdentification &filtered_identification)
 filters a ProteinIdentification corresponding to the given proteins only proteins with the same accession
void filterIdentificationsByExclusionPeptides (const PeptideIdentification &identification, std::vector< String > peptides, PeptideIdentification &filtered_identification)
 removes all peptide hits having a sequence equal to a element in peptides
void filterIdentificationsByRTPValues (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, DoubleReal p_value=0.05)
 Filters the peptide hits according to their predicted rt p-values.
template<class PeakT>
void filterIdentificationsByThresholds (MSExperiment< PeakT > &experiment, DoubleReal peptide_threshold_fraction, DoubleReal protein_threshold_fraction)
 filters an MS/MS experiment corresponding to the threshold_fractions
template<class PeakT>
void filterIdentificationsByScores (MSExperiment< PeakT > &experiment, DoubleReal peptide_threshold_score, DoubleReal protein_threshold_score)
 filters an MS/MS experiment corresponding to the threshold_fractions
template<class PeakT>
void filterIdentificationsByBestNHits (MSExperiment< PeakT > &experiment, UInt n)
 filters an MS/MS experiment corresponding to the best n hits for every spectrum
template<class PeakT>
void filterIdentificationsByProteins (MSExperiment< PeakT > &experiment, std::vector< std::pair< String, String > >proteins)
 filters an MS/MS experiment corresponding to the given proteins


Constructor & Destructor Documentation

IDFilter (  ) 

Constructor.

~IDFilter (  ) 

Destructor.


Member Function Documentation

void filterIdentificationsByThreshold ( const IdentificationType &  identification,
DoubleReal  threshold_fraction,
IdentificationType &  filtered_identification 
) [inline]

filters a ProteinIdentification or PeptideIdentification corresponding to the threshold_fraction

void filterIdentificationsByScore ( const IdentificationType &  identification,
DoubleReal  threshold_score,
IdentificationType &  filtered_identification 
) [inline]

filters a ProteinIdentification or PeptideIdentification corresponding to the threshold_score

If the method higherScoreBetter() returns true for the IdentificationType all hits with a score smaller than threshold_score are removed. Otherwise all hits with a score bigger than threshold_score are removed.

void filterIdentificationsByBestNHits ( const IdentificationType &  identification,
UInt  n,
IdentificationType &  filtered_identification 
) [inline]

filters a ProteinIdentification or PeptideIdentification corresponding to the score.

If the method higherScoreBetter() returns true for the IdentificationType the n highestscoring hits are kept. Otherwise the n lowest scoring hits are kept.

void filterIdentificationsByBestHits ( const PeptideIdentification identification,
PeptideIdentification filtered_identification,
bool  strict = false 
)

filters a PeptideIdentification keeping only the best scoring hits (if strict is set, keeping only the best hit only if it is the only hit with that score)

void filterIdentificationsByProteins ( const PeptideIdentification identification,
std::vector< std::pair< String, String > >  proteins,
PeptideIdentification filtered_identification 
)

filters a PeptideIdentification corresponding to the given proteins

void filterIdentificationsByProteins ( const ProteinIdentification identification,
std::vector< std::pair< String, String > >  proteins,
ProteinIdentification filtered_identification 
)

filters a ProteinIdentification corresponding to the given proteins only proteins with the same accession

void filterIdentificationsByExclusionPeptides ( const PeptideIdentification identification,
std::vector< String peptides,
PeptideIdentification filtered_identification 
)

removes all peptide hits having a sequence equal to a element in peptides

void filterIdentificationsByRTPValues ( const PeptideIdentification identification,
PeptideIdentification filtered_identification,
DoubleReal  p_value = 0.05 
)

Filters the peptide hits according to their predicted rt p-values.

Filters the peptide hits of this ProteinIdentification by the probability (p-value) of a correct ProteinIdentification having a deviation between observed and predicted rt equal or bigger than allowed. If there are unset p_values of the peptide hits the function returns 'true' otherwise 'false'.

void filterIdentificationsByThresholds ( MSExperiment< PeakT > &  experiment,
DoubleReal  peptide_threshold_fraction,
DoubleReal  protein_threshold_fraction 
) [inline]

filters an MS/MS experiment corresponding to the threshold_fractions

void filterIdentificationsByScores ( MSExperiment< PeakT > &  experiment,
DoubleReal  peptide_threshold_score,
DoubleReal  protein_threshold_score 
) [inline]

filters an MS/MS experiment corresponding to the threshold_fractions

void filterIdentificationsByBestNHits ( MSExperiment< PeakT > &  experiment,
UInt  n 
) [inline]

filters an MS/MS experiment corresponding to the best n hits for every spectrum

void filterIdentificationsByProteins ( MSExperiment< PeakT > &  experiment,
std::vector< std::pair< String, String > >  proteins 
) [inline]

filters an MS/MS experiment corresponding to the given proteins


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1