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immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
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repExplore of aa and nt give the same result #313

Open jeitziner opened 2 years ago

jeitziner commented 2 years ago

🐛 Bug

Hi, I was wondering if I missunderstood it but shouldn't repExplore(immdata,.col="nt") and repExplore(immdata,.col="aa") give a different result ? For me it does not. I checked a little bit the code and as I understood it is taking aa and nt only into account when checking the repertoire for length right? If so, could you add this feature for the volume ? Such that we get the Richness (unique cdr3.aa per sample)

Thanks !

Expected behavior

I expect the unique cdr3.aa to be smaller than the nt, it is not the case.

Alexander230 commented 1 year ago

Hi, @jeitziner!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

It may be not a bug, because if the sample doesn't contain any amino acids that are coded by different nucleotide combinations, repExplore() is expected to produce the same results for .col="nt" and .col="aa". If this is not the case, please attach some example data for which the bug happens; it will help me to reproduce and fix it.

Best regards, Aleksandr