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ncborcherding / scRepertoire

A toolkit for single-cell immune profiling
https://www.borch.dev/uploads/screpertoire/
MIT License
311 stars 54 forks source link

clonotypeBias sensible approach to calculating baseline frequency #416

Closed jhjlee closed 1 month ago

jhjlee commented 1 month ago

Hi Nick,

Thanks for the wonderful tool. I have a question about using clonotypeBias (or clonalBias). I have TCR data from multiple donors across multiple tissues. I am wondering what would be the most sensible way to calculate baseline frequency - is it using split.by on donor or tissue information? Thanks.

ncborcherding commented 1 month ago

Hey Joshua,

Could you combine the donor and tissue into a single variable by concatenating them? Not sure if I can give you specific advice as the comparison should be based on the question you are trying to answer.

Please let me know if you have any more information and happy to keep discussing.

Nick