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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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Support for MiXCR 4.1 format #316

Open cwoehle opened 2 years ago

cwoehle commented 2 years ago

Dear immunarch team,

thank you for the nice R package.

I recognized that there is a new release of MiXCR (4.1) with severeal changes and where the default exported clonotypes format does not seem properly recognized by repLoad. (Also the command line execution for MiXCR changed.)

I would be grateful, if you could consider updating this for the next release.

Many thanks & Best wishes, Christian

Alexander230 commented 2 years ago

Hi, Christian!

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

I can update the parser to support the new format; can you, please, send me any example file in this format?

Best regards, Aleksandr

cwoehle commented 2 years ago

Hi Aleksandr,

thank you for the quick reply. Here you find an example file (I added the txt extension, as upload of tsv seems not to be supported): Melanoma_tumor_from_humanized_mice_1.clones_TRAD.tsv.txt

You will recognize that there is a column 'readCount' as well as 'uniqueUMICount'. While the presence of UMI counts may depend on the application, it would be great to be able to make use of it instead of read counts. (Further note that there is support for single cell applications, which may report cell counts (probably as 'uniqueCELLCount'), but which I did not check out yet.)

Best wishes, Christian

Alexander230 commented 2 years ago

Thank you for the example! I will notify you when the support for this format will be ready.

Best wishes, Aleksandr

Alexander230 commented 2 years ago

I've added support for this format, now it's in branch mixcr-format-update. Eventually, it will be merged into dev, and then included into the next release of Immunarch.

You can install Immunarch from this now with these commands:

install.packages(c("devtools", "pkgload"))
devtools::install_github("immunomind/immunarch", ref="mixcr-format-update")
devtools::reload(pkgload::inst("immunarch"))

Also, I've added support for custom count column selection for MiXCR format here; you can use

repLoad("Melanoma_tumor_from_humanized_mice_1.clones_TRAD.tsv.txt", .count = "UniqueUMICount")

And then UniqueUMICount column will be loaded for counts. If you have more question, feel free to ask them!

Best regards, Aleksandr