|
| static void | store (const String &pin_file, const std::vector< PeptideIdentification > &peptide_ids, const StringList &feature_set, const std::string &enz, int min_charge, int max_charge) |
| |
| static std::vector< PeptideIdentification > | load (const String &pin_file, bool higher_score_better, const String &score_name, const StringList &extra_scores, StringList &filenames, String decoy_prefix="", double threshold=0.01, bool SageAnnotation=false) |
| | Loads peptide identifications from a Percolator input file. More...
|
| |
| static String | getScanIdentifier (const PeptideIdentification &pid, size_t index) |
| |
Class for storing Percolator tab-delimited input files.
Loads peptide identifications from a Percolator input file.
This function reads a Percolator input file (pin_file) and returns a vector of PeptideIdentification objects. It extracts relevantinformation such as peptide sequences, scores, charges, annotations, and protein accessions, applying specified thresholds and handling decoy targets as needed. Note: If a filename column is encountered the set of filenames is filled in the order of appearance and PeptideIdentifications annotated with the id_merge_index meta value to link them to the filename (similar to a merged idXML file).
- Parameters
-
| pin_file | he path to the Percolator input file with a .pin extension. |
| higher_score_better | A boolean flag indicating whether higher scores are considered better (true) or lower scores are better (false). |
| score_name | The name of the primary score to be used for ranking peptide hits. |
| extra_scores | A list of additional score names that should be extracted and stored in each PeptideHit. |
| filenames | Will be populated with the unique raw file names extracted from the input data. |
| decoy_prefix | The prefix used to identify decoy protein accessions. Proteins with accessions starting with this prefix are marked as decoys. Otherwise, it assumes that the pin file already contains the correctly annotated decoy status. |
| threshold | A double value representing the threshold for the spectrum_q value. Only spectra with spectrum_q below this threshold are processed. Implemented to allow prefiltering of Sage results. |
| SageAnnotation | A boolean value used to determine if the pin file is coming from Sage or not |
- Returns
- A
std::vector of PeptideIdentification objects containing the peptide identifications.
- Exceptions
-
| <tt>Exception::ParseError</tt> | if any line in the input file does not have the expected number of columns. TODO: implement something similar to PepXMLFile().setPreferredFixedModifications(getModifications_(fixed_modifications_names));
|
1.9.1