used to filter identifications by different criteria More...
#include <OpenMS/FILTERING/ID/IDFilter.h>
Public Member Functions | |
IDFilter () | |
Constructor. More... | |
virtual | ~IDFilter () |
Destructor. More... | |
template<class IdentificationType > | |
void | filterIdentificationsByThreshold (const IdentificationType &identification, DoubleReal threshold_fraction, IdentificationType &filtered_identification) |
filters a ProteinIdentification or PeptideIdentification by only allowing peptides/proteins which reach a score above threshold_fraction * SignificanceThreshold More... | |
template<class IdentificationType > | |
void | filterIdentificationsByScore (const IdentificationType &identification, DoubleReal threshold_score, IdentificationType &filtered_identification) |
filters a ProteinIdentification or PeptideIdentification corresponding to the threshold_score More... | |
template<class IdentificationType > | |
void | filterIdentificationsByBestNHits (const IdentificationType &identification, Size n, IdentificationType &filtered_identification) |
filters a ProteinIdentification or PeptideIdentification corresponding to the score. More... | |
template<class IdentificationType > | |
void | filterIdentificationsByBestNToMHits (const IdentificationType &identification, Size n, Size m, IdentificationType &filtered_identification) |
filters a ProteinIdentification or PeptideIdentification corresponding to the score. More... | |
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) More... | |
void | filterIdentificationsByProteins (const PeptideIdentification &identification, const std::vector< FASTAFile::FASTAEntry > &proteins, PeptideIdentification &filtered_identification, bool no_protein_identifiers=false) |
void | filterIdentificationsByProteins (const ProteinIdentification &identification, const std::vector< FASTAFile::FASTAEntry > &proteins, ProteinIdentification &filtered_identification) |
void | filterIdentificationsByExclusionPeptides (const PeptideIdentification &identification, const std::set< String > &peptides, PeptideIdentification &filtered_identification) |
removes all peptide hits having a sequence equal to a element in peptides More... | |
void | filterIdentificationsByLength (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, Size min_length, Size max_length=UINT_MAX) |
only peptides having a length equal to or greater than 'min_length' will be kept, if 'max_length' is actually greater or equal 'min_length', also only peptides having a length less or equal to 'max_length' will be kept More... | |
void | filterIdentificationsByCharge (const PeptideIdentification &identification, Int charge, PeptideIdentification &filtered_identification) |
only peptides that have a charge equal to or greater than 'charge' will be kept More... | |
void | filterIdentificationsByVariableModifications (const PeptideIdentification &identification, const std::vector< String > &fixed_modifications, PeptideIdentification &filtered_identification) |
only peptides having a variable modification will be kept More... | |
void | removeUnreferencedProteinHits (const ProteinIdentification &identification, const std::vector< PeptideIdentification > peptide_identifications, ProteinIdentification &filtered_identification) |
only protein hits in 'identification' which are referenced by a peptide in 'peptide_identifications' are kept More... | |
void | filterIdentificationsUnique (const PeptideIdentification &identification, PeptideIdentification &filtered_identification) |
if a peptide hit occurs more than once per PSM, only one instance is kept More... | |
void | filterIdentificationsByMzError (const PeptideIdentification &identification, DoubleReal mass_error, bool unit_ppm, PeptideIdentification &filtered_identification) |
filter identifications by deviation to the theoretical mass More... | |
void | filterIdentificationsByRTPValues (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, DoubleReal p_value=0.05) |
Filters the peptide hits according to their predicted rt p-values. More... | |
void | filterIdentificationsByRTFirstDimPValues (const PeptideIdentification &identification, PeptideIdentification &filtered_identification, DoubleReal p_value=0.05) |
Filters the peptide hits according to their predicted rt p-values of the first dimension. More... | |
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 More... | |
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 More... | |
template<class PeakT > | |
void | filterIdentificationsByBestNHits (MSExperiment< PeakT > &experiment, Size n) |
filters an MS/MS experiment corresponding to the best n hits for every spectrum More... | |
template<class PeakT > | |
void | filterIdentificationsByProteins (MSExperiment< PeakT > &experiment, const std::vector< FASTAFile::FASTAEntry > &proteins) |
filters an MS/MS experiment corresponding to the given proteins More... | |
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.
TODO: fix design of filter functions. There will be an error e.g. if input and output points to the same PeptideIdentification.
IDFilter | ( | ) |
Constructor.
|
virtual |
Destructor.
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)
|
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.
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inline |
filters an MS/MS experiment corresponding to the best n hits for every spectrum
References PeptideIdentification::getHits(), ProteinIdentification::getHits(), ExperimentalSettings::getProteinIdentifications(), ExperimentalSettings::setProteinIdentifications(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
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inline |
filters a ProteinIdentification or PeptideIdentification corresponding to the score.
If the method higherScoreBetter() returns true for the IdentificationType the n to m highestscoring hits are kept. Otherwise the n to m lowest scoring hits are kept. This method is useful if a range of higher hits are used for decoy fairness analysis.
void filterIdentificationsByCharge | ( | const PeptideIdentification & | identification, |
Int | charge, | ||
PeptideIdentification & | filtered_identification | ||
) |
only peptides that have a charge equal to or greater than 'charge' will be kept
void filterIdentificationsByExclusionPeptides | ( | const PeptideIdentification & | identification, |
const std::set< String > & | peptides, | ||
PeptideIdentification & | filtered_identification | ||
) |
removes all peptide hits having a sequence equal to a element in peptides
void filterIdentificationsByLength | ( | const PeptideIdentification & | identification, |
PeptideIdentification & | filtered_identification, | ||
Size | min_length, | ||
Size | max_length = UINT_MAX |
||
) |
only peptides having a length equal to or greater than 'min_length' will be kept, if 'max_length' is actually greater or equal 'min_length', also only peptides having a length less or equal to 'max_length' will be kept
void filterIdentificationsByMzError | ( | const PeptideIdentification & | identification, |
DoubleReal | mass_error, | ||
bool | unit_ppm, | ||
PeptideIdentification & | filtered_identification | ||
) |
filter identifications by deviation to the theoretical mass
void filterIdentificationsByProteins | ( | const PeptideIdentification & | identification, |
const std::vector< FASTAFile::FASTAEntry > & | proteins, | ||
PeptideIdentification & | filtered_identification, | ||
bool | no_protein_identifiers = false |
||
) |
filters a PeptideIdentification corresponding to the given proteins PeptideHits with no matching proteins are removed. Matching is done either based on accessions or on sequence (if no accessions are given, or no_protein_identifiers is set)
void filterIdentificationsByProteins | ( | const ProteinIdentification & | identification, |
const std::vector< FASTAFile::FASTAEntry > & | proteins, | ||
ProteinIdentification & | filtered_identification | ||
) |
filters a ProteinIdentification corresponding to the given proteins ProteinHits with no matching proteins are removed. Matching is done based on accessions only
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inline |
filters an MS/MS experiment corresponding to the given proteins
References PeptideIdentification::getHits(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
void filterIdentificationsByRTFirstDimPValues | ( | const PeptideIdentification & | identification, |
PeptideIdentification & | filtered_identification, | ||
DoubleReal | p_value = 0.05 |
||
) |
Filters the peptide hits according to their predicted rt p-values of the first dimension.
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.
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.
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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.
|
inline |
filters an MS/MS experiment corresponding to the threshold_fractions
References PeptideIdentification::getHits(), ProteinIdentification::getHits(), ExperimentalSettings::getProteinIdentifications(), ExperimentalSettings::setProteinIdentifications(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
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inline |
filters a ProteinIdentification or PeptideIdentification by only allowing peptides/proteins which reach a score above threshold_fraction
* SignificanceThreshold
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inline |
filters an MS/MS experiment corresponding to the threshold_fractions
References PeptideIdentification::getHits(), ProteinIdentification::getHits(), ExperimentalSettings::getProteinIdentifications(), ExperimentalSettings::setProteinIdentifications(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
void filterIdentificationsByVariableModifications | ( | const PeptideIdentification & | identification, |
const std::vector< String > & | fixed_modifications, | ||
PeptideIdentification & | filtered_identification | ||
) |
only peptides having a variable modification will be kept
void filterIdentificationsUnique | ( | const PeptideIdentification & | identification, |
PeptideIdentification & | filtered_identification | ||
) |
if a peptide hit occurs more than once per PSM, only one instance is kept
void removeUnreferencedProteinHits | ( | const ProteinIdentification & | identification, |
const std::vector< PeptideIdentification > | peptide_identifications, | ||
ProteinIdentification & | filtered_identification | ||
) |
only protein hits in 'identification' which are referenced by a peptide in 'peptide_identifications' are kept
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5 |