prepDB: Create a antigen specific T-cells database

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Create a antigen specific T-cells database

Description

This function takes as input path to the flat file versions of IEDB, McPAS-TCR, and VdjDB slim in that order and generates an RDA file of all T-cells and B-cells recorded to show antigenic specificity in these three databases. This is a script for internal use and will be run once every six months to update the databases. The flat files for this function can be downloaded at the following links:

1. IEDB: https://www.iedb.org/downloader.php?file_name=doc/receptor_full_v3.zip

2. McPAS-TCR: http://friedmanlab.weizmann.ac.il/McPAS-TCR/

3. VdjDB: https://github.com/antigenomics/vdjdb-db/releases Note: Here the vdjdb.slim.txt is used as the input Note: The order of the input matters, please provide the flat file paths in this order IEDB, McPAS-TCR, VdjDB.

Usage

prepDB(db_path = NULL)

Arguments

db_path

Path to IEDB, McPAS-TCR and VdjDB

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.