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ncborcherding / scRepertoire

A toolkit for single-cell immune profiling
https://www.borch.dev/uploads/screpertoire/
MIT License
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Regular expression used for quietTCRgenes.R #369

Closed user-pagh closed 6 months ago

user-pagh commented 6 months ago

Hi Nick and team.

This is more of a comment than an issue. I looked through past posts on this page and couldn't find any comments on the regular expression used for Trex::quietTCRgenes.R().

According to https://rdrr.io/github/ncborcherding/Trex/src/R/quietTCRgenes.R ("built on April 27, 2024, 5:02 a.m") the regular expression used for this function is:

unwanted_genes <- "^TR[ABDG][VDJ]"

This also filters away the gene "TRADD" (Tumor necrosis factor receptor type 1-associated DEATH domain protein). I have previously used the following to avoid this: "^TR[ABDG][VDJ][^D]"

It's a tiny detail - and TRADD is so far the only case of non-TCR genes I've seen included with the given regular expression that you propose.

Kind regards, Nikolaj

ncborcherding commented 6 months ago

Hey Nikolaj,

Thanks for the suggestions - I have incorporated into the dev version of Trex and will push it to the master branch when I am done with some additional changes.

Nick