How do I combine or integrate my VDJ data for TCR and BCR with seurat object?

Question

[Jaber]

Greetings I am analyzing V(D)J single-cell data from the 10x Genomics dataset: https://www.10xgenomics.com/datasets/nsclc-tumor-1-standard-5-0-0

This dataset comes from a single sample (non-small cell lung cancer tumor, ~7,800 cells). I am working with both TCR and BCR data and using scRepertoire. Below is my current workflow and some specific questions:

library(scRepertoire)

1. Loading the files

tcr <- read.csv("Data/VDJ/vdj_v1_hs_nsclc_multi_5gex_t_b_vdj_t_filtered_contig_annotations.csv")
bcr <- read.csv("Data/VDJ/vdj_v1_hs_nsclc_multi_5gex_t_b_vdj_b_filtered_contig_annotations.csv")

2. Combine tcr and bcr

combined_vdj <-  What is the proper way to combine both TCR and BCR into one object?

3. I now want to combine the combined_vdj with seurat object

    seurat_obj_filtered <- combineExpression(
combined_vdj,
  seurat_obj_filtered,
  cloneCall = "gene",
  groupBy = ?)

Should "groupBy" be ~1 since it's a single sample?

Questions

1. How should I combine both TCR and BCR VDJ files into one combined_vdj object using scRepertoire?

1. Should I use combineTCR() separately and then merge manually? Or is there a wrapper for combining both?

1. How should I set the groupBy argument in combineExpression() given

   that I have only one sample? Should I set groupBy = NULL, groupBy = "sample", or groupBy = ~1?
   

2. Is cloneCall = "gene" the most appropriate option to track clonal

       diversity for both TCR and BCR together?
   

1. Would aa or nt be more informative in some settings?

1. Is scRepertoire considered the best or most comprehensive R package

   for analyzing TCR/BCR data integrated with scRNA-seq? Or would you recommend complementing it with other tools (e.g., immunarch)?
   

1. Are there best practices or reference pipelines for combining TCR

       and BCR data from the same sample in single-cell VDJ-seq analysis?
   

Any help or recommendations would be deeply appreciated. Thank you! — Jaber Husam Jaradat.