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

In immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

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)

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

immunarch documentation built on Dec. 28, 2022, 2:59 a.m.