#include <OpenMS/FILTERING/ID/IDFilter.h>
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 |
IDFilter | ( | ) |
Constructor.
~IDFilter | ( | ) |
Destructor.
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
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |