cellrangerVDJdb

Database and R interface to load and query assembled VDJ sequences from CellRanger. Currently supports loading data from CellRanger multi output for T cell receptors, expecting the output to be in a directory named as "multi/__s__/outs/per_sample_outs/__s__/vdj_t/", where __s__ represents a sample name. Other directory structures may be specified, and would work as long as the correct files are to be found there. The expected CellRanger output files are:

• airr_rearrangement.tsv
• cell_barcodes.json
• clonotypes.csv
• consensus_annotations.csv
• filtered_contig_annotations.csv

An ER diagram describing the created database structure can be found here: ER diagram

Usage

It is a requirement that PostgreSQL is already setup and running.

First, specify database connection information and a desired database name:

dbname = "vdj_t"
port = 5432
user = "postgres"
password <- .rs.askForPassword("Database Password:")

Then, create an empty database and set up all tables to store the data:

library(cellrangerVDJdb)

create_database(user = user, 
                dbname = dbname, 
                password = password,
                psql_path = psql_path)

create_tables(user = user, 
                dbname = dbname, 
                password = password,
                psql_path = psql_path)

Test connecting to the database from R:

test_connection(dbname, port, user, password)

Load data into the database (here, "sname" represents a sample name):

load_from_cellranger_vdj_t(
    sname = sname, 
    resultsdir = "/path/to/10x/results/",
    cellranger_dir_structure = paste0("multi/", "__s__", 
                                      "/outs/per_sample_outs/", "__s__", 
                                      "/vdj_t/"), 
    outdir = "loading_commands",
    dbname = dbname, 
    user = user, 
    password = password, 
    psql_path = "/Library/PostgreSQL/15/bin/psql")

Connect and run a query:

con <- connect(dbname, port, user, password)

res <- query(con, "SELECT DISTINCT clone_id, sample_id FROM airr_rearrangement")

dbDisconnect(con)

> head(res)
       clone_id sample_id
1 clonotype1957        A2
2  clonotype960        7A
3  clonotype815        A2
4  clonotype368        E5
5 clonotype2586        A2
6  clonotype742        6B