Man pages for vladpetyuk/MSnID
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
| accessions | Non-redundant list of accession (protein) identifiers |
| add_mod_symbol | Annotates peptide sequences with modification symbols |
| apply_filter | Filters the MS/MS identifications |
| assess_missed_cleavages | Counts the missing cleavage sites within the peptides... |
| assess_termini | Checks if the peptide termini conforms with cleavage... |
| compute_accession_coverage | Compute accession coverage from identified peptides |
| correct_peak_selection | Corrects wrong selection of monoisotopic peak |
| data | Example mzIdenML File and MSnID Object |
| evaluate_filter | Filters the MS/MS identifications |
| extract_sequence_window | Extracts +/-7 amino acids to the PTM |
| fetch_conversion_table | Fetches conversion table form one type of identifiers to... |
| id_quality | Identification quality |
| infer_parsimonious_accessions | Eliminates Redundancy in Peptide-to-Protein Mapping |
| map_mod_sites | Maps the modifications to protein sequence |
| map_peptide_position | Maps the peptide location(s) to protein sequence |
| mass_measurement_error | Computes error of the parent ion mass to charge measurement |
| MSnID-class | The "MSnID" Class for Mass Spectrometry Based Proteomics... |
| MSnIDFilter-class | The "MSnIDFilter" Class for Handling MS/MS Criteria,... |
| MSnID-package | MSnID: Utilities for Handling MS/MS Identifications |
| optimize_filter | Filter criteria optimization to maximize the number of... |
| peptides | Non-redundant list of peptides |
| plot_protein_coverage | Shows the peptide location(s) on the protein sequence |
| psms | Peptide-to-spectrum matches |
| read_mzIDs | Populates MS/MS results table from mzIdentML files |
| recalibrate | Post-experimental recalibration of observed mass to charge... |
| remap_accessions-method | Changes accessions from one protein id to another |
| remap_fasta_entry_names | Remapping entries in FASTA file |
| report_mods | Lists modification masses in the MSnID object |
