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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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clonesizedistribution() error message #185

Closed Lucy13579 closed 1 year ago

Lucy13579 commented 2 years ago

Hello,

Thank you so much for creating such a great package, it is making my life much easier! I am analysing 5P 10x data from human T cells and am using scRepertoire to compare the TCR repertoire between the different clusters in my Seurat object. When I try to run clonesizedistribution() I get the following error:

clonesizeDistribution(my_scr_object, cloneCall = "gene+nt", method = "ward.D2") Error in gammfit[[bestfit]] : attempt to select less than one element in get1index

I tried adding the threshold parameter as you suggested in issue #128 but got the same error. Please would you advise?

Thanks again

Lucy

ncborcherding commented 2 years ago

Hey Lucy,

Apologies to you for the issue - this seems to relate to the data structure and internal PowerTCR function called fdiscgammagpd(). I am not able to recreate the issue with the vignette data or any of the data I have available.

Would you be willing to send a copy of your seurat object (or a sampled seurat object) to see if I can find/fix the issue? If not, I will try to troubleshoot from my end.

Thanks, Nick

ncborcherding commented 1 year ago

Follow up on this - the fdiscgammagpd() would not fit the data. After troubleshooting, there does not seem to be a way to force the distribution calculation and probably should be an error brought up with PowerTCR. Apologies if any other user is experiencing this.