Helper class for peptide and protein quantification based on feature data annotated with IDs. More...
#include <OpenMS/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.h>
Classes | |
| struct | PeptideData |
| Quantitative and associated data for a peptide. More... | |
| struct | ProteinData |
| Quantitative and associated data for a protein. More... | |
| struct | Statistics |
| Statistics for processing summary. More... | |
Public Types | |
| typedef std::map< UInt64, DoubleReal > | SampleAbundances |
| Mapping: sample ID -> abundance. | |
| typedef std::map< AASequence, PeptideData > | PeptideQuant |
| Mapping: peptide sequence (modified) -> peptide data. | |
| typedef std::map< String, ProteinData > | ProteinQuant |
| Mapping: protein accession -> protein data. | |
Public Member Functions | |
| PeptideAndProteinQuant () | |
| Constructor. | |
| ~PeptideAndProteinQuant () | |
| Destructor. | |
| void | quantifyPeptides (FeatureMap<> &features) |
| Compute peptide abundances from data in a feature map. | |
| void | quantifyPeptides (ConsensusMap &consensus) |
| Compute peptide abundances from data in a consensus map. | |
| void | quantifyProteins (const ProteinIdentification &proteins=ProteinIdentification()) |
| Compute protein abundances. | |
| const Statistics & | getStatistics () |
| Get summary statistics. | |
| const PeptideQuant & | getPeptideResults () |
| Get peptide abundance data. | |
| const ProteinQuant & | getProteinResults () |
| Get protein abundance data. | |
Private Member Functions | |
| PeptideHit | getAnnotation_ (std::vector< PeptideIdentification > &peptides) |
| Get the "canonical" annotation (a single peptide hit) of a feature/consensus feature from the associated list of peptide identifications. | |
| void | quantifyFeature_ (const FeatureHandle &feature, const PeptideHit &hit) |
| Gather quantitative information from a feature. | |
| template<typename T > | |
| void | orderBest_ (const std::map< T, SampleAbundances > abundances, std::vector< T > &result) |
| Order keys (charges/peptides for peptide/protein quantification) according to how many samples they allow to quantify, breaking ties by total abundance. | |
| void | quantifyPeptides_ () |
| Compute overall peptide abundances. | |
| void | normalizePeptides_ () |
| Normalize peptide abundances across samples by (multiplicative) scaling to equal medians. | |
| String | getAccession_ (const std::set< String > &pep_accessions, std::map< String, String > &accession_to_leader) |
| Get the "canonical" protein accession from the list of protein accessions of a peptide. | |
| void | countPeptides_ (std::vector< PeptideIdentification > &peptides) |
| Count the number of identifications (best hits only) of each peptide sequence. | |
| void | updateMembers_ () |
| Clear all data when parameters are set. | |
Private Attributes | |
| Statistics | stats_ |
| Processing statistics for output in the end. | |
| PeptideQuant | pep_quant_ |
| Peptide quantification data. | |
| ProteinQuant | prot_quant_ |
| Protein quantification data. | |
Detailed Description
Helper class for peptide and protein quantification based on feature data annotated with IDs.
This class is used by ProteinQuantifier. See there for further documentation.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| top | int | 3 | min: 0 | Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all) |
| average | string | median | median, mean, sum | Averaging method used to compute protein abundances from peptide abundances |
| include_all | string | false | true, false | Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1) |
| filter_charge | string | false | true, false | Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge; for proteins, abundances will be computed based only on the most prevalent charge of each peptide. By default, abundances are summed over all charge states. |
| consensus:normalize | string | false | true, false | Scale peptide abundances so that medians of all samples are equal |
| consensus:fix_peptides | string | false | true, false | Use the same peptides for protein quantification across all samples. With 'top 0', all peptides that occur in every sample are considered. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!). |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Member Typedef Documentation
| typedef std::map<AASequence, PeptideData> PeptideQuant |
Mapping: peptide sequence (modified) -> peptide data.
| typedef std::map<String, ProteinData> ProteinQuant |
Mapping: protein accession -> protein data.
| typedef std::map<UInt64, DoubleReal> SampleAbundances |
Mapping: sample ID -> abundance.
Constructor & Destructor Documentation
Constructor.
| ~PeptideAndProteinQuant | ( | ) | [inline] |
Destructor.
Member Function Documentation
| void countPeptides_ | ( | std::vector< PeptideIdentification > & | peptides | ) | [private] |
Count the number of identifications (best hits only) of each peptide sequence.
The peptide hits in peptides are sorted by score in the process.
| String getAccession_ | ( | const std::set< String > & | pep_accessions, | |
| std::map< String, String > & | accession_to_leader | |||
| ) | [private] |
Get the "canonical" protein accession from the list of protein accessions of a peptide.
- Parameters:
-
pep_accessions Protein accessions of a peptide accession_to_leader Captures information about indistinguishable proteins (maps accession to accession of group leader)
If there is no information about indistinguishable proteins (from protXML) available, a canonical accession exists only for proteotypic peptides - it's the single accession for the respective peptide.
Otherwise, a peptide has a canonical accession if it maps only to proteins of one indistinguishable group. In this case, the canonical accession is that of the group leader.
If there is no canonical accession, the empty string is returned.
| PeptideHit getAnnotation_ | ( | std::vector< PeptideIdentification > & | peptides | ) | [private] |
Get the "canonical" annotation (a single peptide hit) of a feature/consensus feature from the associated list of peptide identifications.
Only the best-scoring peptide hit of each ID in peptides is taken into account. The hits of each ID must already be sorted! If there's more than one ID and the best hits are not identical by sequence, or if there's no peptide ID, an empty peptide hit (for "ambiguous/no annotation") is returned. Protein accessions from identical peptide hits are accumulated.
| const PeptideQuant& getPeptideResults | ( | ) |
Get peptide abundance data.
| const ProteinQuant& getProteinResults | ( | ) |
Get protein abundance data.
| const Statistics& getStatistics | ( | ) |
Get summary statistics.
| void normalizePeptides_ | ( | ) | [private] |
Normalize peptide abundances across samples by (multiplicative) scaling to equal medians.
| void orderBest_ | ( | const std::map< T, SampleAbundances > | abundances, | |
| std::vector< T > & | result | |||
| ) | [inline, private] |
Order keys (charges/peptides for peptide/protein quantification) according to how many samples they allow to quantify, breaking ties by total abundance.
The keys of abundances are stored ordered in result, best first.
| void quantifyFeature_ | ( | const FeatureHandle & | feature, | |
| const PeptideHit & | hit | |||
| ) | [private] |
Gather quantitative information from a feature.
Store quantitative information from feature in member pep_quant_, based on the peptide annotation in hit. If hit is empty ("ambiguous/no annotation"), nothing is stored.
| void quantifyPeptides | ( | ConsensusMap & | consensus | ) |
Compute peptide abundances from data in a consensus map.
Parameters should be set before using this method, as setting parameters will clear all results.
| void quantifyPeptides | ( | FeatureMap<> & | features | ) |
Compute peptide abundances from data in a feature map.
Parameters should be set before using this method, as setting parameters will clear all results.
| void quantifyPeptides_ | ( | ) | [private] |
Compute overall peptide abundances.
Based on quantitative data for individual charge states (derived from annotated features) in member pep_quant_, compute overall abundances for all peptides and store them also in pep_quant_.
| void quantifyProteins | ( | const ProteinIdentification & | proteins = ProteinIdentification() |
) |
Compute protein abundances.
Peptide abundances must be computed first with quantifyPeptides. Optional information about groups of indistinguishable proteins (from ProteinProphet) can be supplied via proteins.
| void updateMembers_ | ( | ) | [private, virtual] |
Clear all data when parameters are set.
Reimplemented from DefaultParamHandler.
Member Data Documentation
PeptideQuant pep_quant_ [private] |
Peptide quantification data.
ProteinQuant prot_quant_ [private] |
Protein quantification data.
Statistics stats_ [private] |
Processing statistics for output in the end.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1 |