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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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repLoad question: Warning: found NAs in clonal counts. Setting them to 1's. #362

Closed JHYSiu closed 1 year ago

JHYSiu commented 1 year ago

I am unable to calculate clones when loading AIRR data. The data is 10x TCR data that I have QC'd and saved as AIRR file (see sample attached) for loading.

Code used: combined_immdata <- repLoad(file_path, .mode = "paired")

What columns of data are being used to calculate the clones? test_TCR_airr.csv

Thanks!

zelenkt commented 1 year ago

The same problem occurs when using AIRR data generated by TRUST4 (from bulk RNA-seq). I assume the problem is caused by the fact that the TRUST4 report contains consensus_count whereas Immunarch expects only duplicate_count.

JHYSiu commented 1 year ago

thanks! replaced my umi_count column with duplicate_count, and it works.