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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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Using expression2List() #440

Closed zoqaiyum closed 2 weeks ago

zoqaiyum commented 2 weeks ago

Hi,

I have v2.1.0 of the package. I understand that expression2List() function has been deprecated, however a slightly older tutorial I am using mentions this function in one of lines of code. Is there any way to use this again? Are there any alternatives if this function is gone forever?

Thank you!

ncborcherding commented 2 weeks ago

@zoqaiyum,

expression2List() was causing a lot of questions from users, so the choice was made to deprecate it and support single-cell objects and the output of combineTCR() & combineBCR() for all functions.

That being said, it does still exist and you can access it via scRepertoire:::.expresion2List(). Notice 2 small changes here, we places a new . to mark it as an internal function and you can access via the 3 colons :::.

Hope that helps and good luck with your analysis.

Nick

zoqaiyum commented 2 weeks ago

Hi @ncborcherding ,

I managed to access it, however when I call on group = myvariable, it gives me an error and says unused argument. Please see code below:

mergedseurat2_example_tcrbycluster <- scRepertoire:::.expression2List(mergedseurat2_example, group = "clusters_names_tissue")

The error below: Error in scRepertoire:::.expression2List(mergedseurat2_example, group = "clusters_names_tissue") : unused argument (group = "clusters_names_tissue")

If I try running this without the group argument completely, so just the scRepertoire:::.expression2List(mergedseurat2_example), I get the following:

Error in scRepertoire:::.expression2List(mergedseurat2_example) : argument "split.by" is missing, with no default

It appears that I need a split.by argument instead of group? Any insights would be helpful!

Qile0317 commented 2 weeks ago

@zoqaiyum Yes, just use split.by or just omit the named argument. @ncborcherding I'll do a PR to re-export expression2List but with either a deprecation warning or keeping it defunct.