The goal of TrustVDJ is to read immune repertoire data, especially from TRUST4, 10x Genomics cellranger or AIRR format results.
TrustVDJ is available on CRAN
install.packages('TrustVDJ')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