immunarch (version 0.9.1)

dbLoad: Load clonotype databases such as VDJDB and McPAS into the R workspace

Description

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/

Usage

dbLoad(.path, .db, .species = NA, .chain = NA, .pathology = NA)

Value

Data frame with the input database records.

Arguments

.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.

Examples

# Example file path
file_path <- paste0(system.file(package = "immunarch"), "/extdata/db/vdjdb.example.txt")

# Load the database with human-only TRB-only receptors for all known antigens
db <- dbLoad(file_path, "vdjdb", "HomoSapiens", "TRB")
db