README.md

In HatsuneCode/TrustVDJ: Tools for Immune Repertoire Analysis

TrustVDJ

The goal of TrustVDJ is to read immune repertoire data, especially from TRUST4, 10x Genomics cellranger or AIRR format results.

Installation

1. TrustVDJ is available on CRAN:

install.packages('TrustVDJ')

1. Install TrustVDJ using devtools:

devtools::install_github('HatsuneCode/TrustVDJ')

*** Maybe dependency ‘Biostrings’ is not available:

install.packages('BiocManager')
BiocManager::install('Biostrings')

Version

• v0.1.0: initial release.
• v0.1.1: fix bug in build_IMGT_reference: when same gene name, combine their sequences.

Example

There are some basic examples showing how to read 10x/TRUST4 data commonly:

library(TrustVDJ)
## basic example code

# 10x cellranger:
airr10x   = system.file('extdata', '10x_airr_rearrangement.tsv.gz', package = 'TrustVDJ')
contig10x = system.file('extdata', '10x_filtered_contig_annotations.csv.gz', package = 'TrustVDJ')
vdj10x    = Read10x(airr_file = airr10x, contig_file = contig10x, verbose = FALSE)
summary(vdj10x[,1:3])
#>    cell_id            clone_id         sequence_id       
#>  Length:40          Length:40          Length:40         
#>  Class :character   Class :character   Class :character  
#>  Mode  :character   Mode  :character   Mode  :character

# TRUST4:
airrTrust = system.file('extdata', 'TRUST4_airr.tsv.gz', package = 'TrustVDJ')
bcTrust   = system.file('extdata', 'TRUST4_barcode_report.tsv.gz', package = 'TrustVDJ')
vdjTrust  = ReadTrust(airr_file = airrTrust, barcode_report_file = bcTrust, verbose = FALSE)
summary(vdjTrust[,1:3])
#>  sequence_id          sequence           rev_comp        
#>  Length:3245        Length:3245        Length:3245       
#>  Class :character   Class :character   Class :character  
#>  Mode  :character   Mode  :character   Mode  :character

HatsuneCode/TrustVDJ documentation built on Aug. 13, 2022, 9:36 p.m.