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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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Incorrect parsing of AIRR files #387

Open DoaneAS opened 1 year ago

DoaneAS commented 1 year ago

🐛 Bug

Using repLoad with AIRR format files (e.g. output from Change-O] does not retain clone IDs (clone_id column) and incorrectly assigns a value of 1 to the Clones variable.

To Reproduce

Steps to reproduce the behavior:

  1. repLoad("sample_db-pass_parse-select_clone-pass_germ-pass.tsv") or other AIRR rearrangement file.

Expected behavior

Either retain the clone_id variable from the AIRR formatted file to allow for counting, or summarize clone counts into a different table.

martuskaR commented 7 months ago

Hello,

I am also facing an issue with repLoad(). I have BD Rhapsody full length TCR data. Downloaded AIRR format files and I tried loading them to Immunarch. The column 'Barcode' is missing from the object$data. This doesn't allow me to do any analysis on my object. Is this something that can be fixed by manipulation, or is it a bug? Thanks!