The function automatically detects the database format and loads it into R. Additionally, the function provides a general query interface to databases that allows filtering by species, chain types (i.e., locus) and pathology (i.e., antigen species).
Currently we support three popular databases:
VDJDB - https://github.com/antigenomics/vdjdb-db
McPAS-TCR - http://friedmanlab.weizmann.ac.il/McPAS-TCR/
TBAdb from PIRD - https://db.cngb.org/pird/tbadb/
dbLoad(.path, .db, .species = NA, .chain = NA, .pathology = NA)
.path | Character. A path to the database file, e.g., "/Users/researcher/Downloads/McPAS-TCR.csv". |
---|---|
.db | Character. A database type: either "vdjdb", "vdjdb-search", "mcpas" or "tbadb". "vdjdb" for VDJDB; "vdjdb-search" for search table obtained from the web interface of VDJDB; "mcpas" for McPAS-TCR; "tbadb" for PIRD TBAdb. |
.species | Character. A string or a vector of strings specifying which species need to be in the database, e.g., "HomoSapiens". Pass NA (by default) to load all available species. |
.chain | Character. A string or a vector of strings specifying which chains need to be in the database, e.g., "TRB". Pass NA (by default) to load all available chains. |
.pathology | Character. A string or a vector of strings specifying which disease, virus, bacteria or any condition needs to be in the database, e.g., "CMV". Pass NA (by default) to load all available conditions. |
Data frame with the input database records.