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

dbLoad {immunarch} | R Documentation

## 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/tbadb/

### Usage

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

### 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.

### Value

Data frame with the input database records.

### 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

[Package immunarch version 0.6.5 Index]