Clarification + Documentation

[shreyii]

Hi Team,
I have two questions.

1. I get the same values when I run GeneUsage for TRAV and TRBV, and similarly the same data frame output for TRAJ and TRBJ. There should be variation in the alpha and beta chains of the TCR returning different clonotype values and sequences. Kindly clarify.
   

2. I'm looking for detailed documentation about the GeneUsage feature in the package. I want to get a hold of how the matching/alignments take place to give an output of the TRBV sequences. Understanding the algorithm behind which it's run might help validate no loss of sequences - since our objective centers around novelty.

[vadimnazarov]

Hi @shreyarajasekar

Thank you for opening the issue. Could you share the code that you use to run geneUsage please?

The docs are available on the website: https://immunarch.com/reference/geneUsage.html
Or you could run the following command in the R console: ?geneUsage

I'm open to scheduling a short call to discuss this issue over Zoom if this accelerates things.

[shreyii]

Hi @vadimnazarov thanks for the prompt response, appreciate it.
A quick Zoom call would be great.
Here's what I ran.

I've gone through the documentation that exists, but would be helpful to have a deeper insight into the algorithms behind it.

[shreyii]

Hi @vadimnazarov, following up regarding getting the same alignment for alpha and beta sequences.