agdb: Antigen database

In acorg/acutilsLite: A package for working with CPE databases

Description

Antigen database

Details

The antigen database is ultimately stored as a json file with fields:

1. id

2. strain

3. long

4. aliases

5. wildtype

6. type

7. subtype

8. lineage

9. isolation

10. genes

11. parent_id

12. alterations

13. passage

14. comments

15. groups

16. meta

Not all fields are filled for all antigens.

In R, this is converted to a list of environments (see ?ag) with the above fields, plus:

1. A ag$.parent entry, which is the database entry for the parent antigen (defined by the backbone).

2. ag$alteration$.parent entries for each gene that is not inherited from ag$.parent (for recombinant viruses).

acorg/acutilsLite documentation built on Feb. 19, 2021, 4:56 p.m.