How to get the sequences of hyper-expanded clonotypes when running clonalHomeostasis?

[linqy-immune]

Hi Nick, @ncborcherding
Thank you again for your development and maintenance for scRepertoire, such an amazing and powerful package!
Recently I have analyzed my data by scRepertoire and everything is ok. But it occurs to me that whether we can get the specific clone information after running clonalHomeostasis. For instance, how can we get the clones hyperexpanded in P17B?

By the way, I wonder whether it is possible to get such volcano plot to compare clonal expansion in scRepertoire? If not, could you please give me some suggestions?

(The figure was from https://sci-hub.se/10.1016/j.immuni.2021.02.014)

Looking forward to your reply.
Thanks and best regards,
Linqy

[ncborcherding]

Hey @linqy-immune,

Thanks for reaching out!

In terms of your questions - if you use combineExpression() the groupings should be in your meta data of the single-cell object. As of right now, there it would be difficult to do this with just the output of combineBCR() or combineTCR() - but it is a good suggestion for future enhancements.

I am working on expanding statistical support for differential motifs and clones in a companion package for scRepertoire. Right now, you should be able to replicate most of that analysis using edgeR. But I will let you know when I have something more concrete to use.

Nick

[linqy-immune]

Got it. Thank you for your quick reply! Looking forward to the companion package.
Thank you soooo much!!! @ncborcherding