| MSnID-package | MSnID: Utilities for Handling MS/MS Identifications |
| $-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| $-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| $<--method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| $<--method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| accessions | Non-redundant list of accession (protein) identifiers |
| accessions-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| add_mod_symbol | Annotates peptide sequences with modification symbols |
| add_mod_symbol-method | Annotates peptide sequences with modification symbols |
| apply_filter | Filters the MS/MS identifications |
| apply_filter-method | Filters the MS/MS identifications |
| as.numeric-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| assess_missed_cleavages | Counts the missing cleavage sites within the peptides sequence |
| assess_missed_cleavages-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| assess_termini | Checks if the peptide termini conforms with cleavage specificity |
| assess_termini-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| class:MSnID | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| class:MSnIDFilter | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| coerce-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| correct_peak_selection | Corrects wrong selection of monoisotopic peak |
| correct_peak_selection-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| c_elegans | Example mzIdenML File and MSnID Object |
| dim-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| evaluate_filter | Filters the MS/MS identifications |
| evaluate_filter-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| fetch_conversion_table | Fetches conversion table form one type of identifiers to another |
| id_quality | Identification quality |
| id_quality-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| infer_parsimonious_accessions | Eliminates Redundancy in Peptide-to-Protein Mapping |
| infer_parsimonious_accessions-method | Eliminates Redundancy in Peptide-to-Protein Mapping |
| length-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| map_mod_sites | Maps the modifications to protein sequence |
| map_mod_sites-method | Maps the modifications to protein sequence |
| mass_measurement_error | Computes error of the parent ion mass to charge measurement |
| mass_measurement_error-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| MSnID | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| MSnID-class | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| MSnIDFilter | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| MSnIDFilter-class | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| msnidObj | Example mzIdenML File and MSnID Object |
| names-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| names-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| optimize_filter | Filter criteria optimization to maximize the number of identifications given the FDR upper threshold |
| optimize_filter-method | Filter criteria optimization to maximize the number of identifications given the FDR upper threshold |
| peptides | Non-redundant list of peptides |
| peptides-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| proteins | Non-redundant list of accession (protein) identifiers |
| proteins-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| psms | Peptide-to-spectrum matches |
| psms-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| psms<- | Peptide-to-spectrum matches |
| psms<--method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| read_mzIDs | Populates MS/MS results table from mzIdentML files |
| read_mzIDs-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| recalibrate | Post-experimental recalibration of observed mass to charge ratios |
| recalibrate-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| remap_accessions | Changes accessions from one protein id to another |
| 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 |
| report_mods-method | Lists modification masses in the MSnID object |
| show-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| show-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| update-method | The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
| [[-method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
| [[<--method | The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |