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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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quietBCRgenes not compatible with Seurat v5 #434

Closed timothyjtan closed 3 weeks ago

timothyjtan commented 3 weeks ago

I am following the example here, using Seurat v5.0.2: https://www.borch.dev/uploads/screpertoire/articles/ibex#formation-of-the-single-cell-object, and when running this segment

Processing RNA

DefaultAssay(MIS.sample) <- 'RNA' MIS.sample <- NormalizeData(MIS.sample) %>% FindVariableFeatures() %>% quietBCRgenes() %>% ScaleData() %>% RunPCA(verbose = FALSE)

I run into an error:

Error in is.factor(x) : no slot of name "var.features" for this object of class "Assay5"

To figure out where the error occurs, I removed the piping, and performed each step one at a time:

MIS.sample <- NormalizeData(MIS.sample) MIS.sample <- FindVariableFeatures(MIS.sample, selection.method = "vst", nfeatures = 3000) MIS.sample <- quietBCRgenes(MIS.sample, assay = "RNA")

After running quietBCRgenes, I get the error

Error in is.factor(x) : no slot of name "var.features" for this object of class "Assay5"

I am using the following: RStudio v2024.09.0+375 R v4.4.1 Seurat v5.1.0 scRepertoire v2.0.5 scCustomize v2.1.2

ncborcherding commented 3 weeks ago

@timothyjtan

Thanks for the issue - I am in the middle of updating both Ibex and Trex to be compatible with all versions of Seurat. Should be out by the end of November (I am training some additional models as we speak).

Nick

timothyjtan commented 2 weeks ago

Hey Nick, thanks for letting me know, and looking forward to the release for Seurat v5 compatibility! In the meantime, will using Convert_Assay from scCustomize to change the version of the 'RNA' assay of the Seurat object to v3 affect downstream analysis with Ibex? I am integrating Ibex/scRepertoire with Seurat for combined analysis of RNA, ADT, and V(D)J. Thanks!