Ambiguous Gene Usage in TRBD

[ShaowenJ]

❓ Questions and Help

Hi, I was curious whether the ambiguity of nomenclature ("TRBD1, TRBD2" and "TRBD2, TRBD1") in the below figure are caused from the MIXCR input? or the geneUsage function from the immunarch package?

file_path = "/workdir/sj657/lymph_node/notebooks/immunarch_dir/TRB/"
trb_mixcr <- repLoad(file_path)
trbj <- geneUsage(trb_mixcr$data, "musmus.trbd", .norm=T,)
plt = vis(trbj)
plt

Thanks!

[ShaowenJ]

I think I found the argument with the .ambig; but what's the difference between "exc" and "maj"? Thanks again,

[vadimnazarov]

Hi ShaowenJ,

"exc" means excluding those D segments which are in the musmus.trbd library. Maj means taking only the first one, so "TRBD1" from "TRBD1,TRBD2"

https://immunarch.com/reference/geneUsage.html