Man pages for philliplab/EpitopeMatcher
Epitope Matcher
| BETWEEN10 | HIV Scoring Matrix 10 for between host evolution |
| BETWEEN38 | HIV Scoring Matrix 38 for between host evolution |
| build_scoring_jobs | Builds scoring jobs from pre-processed inputs |
| dot-sequence_comparison_stats | Internal function lists information about the alignment... |
| epitope_found | A function that indicates if an epitope was found in the... |
| find_epitope_in_ref | Finds the position of the epitope in the reference sequence |
| flatten_lanl_hla | Flattens the LANL HLA file |
| get_epitope-methods | Returns the epitope associated with a scoring_job |
| get_hla_details-methods | Returns the hla details associated with a scoring_job |
| get_hla_genotype-methods | Returns the hla genotype associated with a scoring_job |
| get_patient_ids-methods | Returns the ids of the patients in the data structure |
| get_set_of_test_data | Get full set of test data |
| get_test_lanl_hla_data | A function that returns a test lanl hla genotype dataset |
| get_test_patient_hla_data | A function that returns a test patient hla dataset |
| get_test_query_alignment | A function that returns a test query alignment |
| LANL_HLA_data | The class for the data from LANL that describe the HLA... |
| list_scores_to_compute | Processes the three input files (query_alignment, patient_hla... |
| match_epitopes | Computes similarities between certain epitopes and sequences |
| match_patient_hla_to_query_alignment | Matches the patient_hla data to the query sequence to check... |
| Patient_HLA | The class for the data that describes which patients have... |
| read_lanl_hla | A function that reads a HLA genotype specification file |
| read_patient_hla | A function that reads a patient HLA genotype specification... |
| read_query_alignment | Reads in the query alignment |
| run_EpitopeMatcher_app | Runs the shiny app for this package |
| score_all_epitopes | Given a list of scoring jobs, compute the similarities |
| score_epitope | Computes the similarities between the epitope and the... |
| Scoring_Job | A class that contains all the required information to run an... |
| WITHIN5 | HIV Scoring Matrix 5 for within host evolution |
