Seurat V5 - var.features

[Dooo0k]

hello.

I am currently trying to check hierarchical clustering, but I have confirmed that var.features data does not exist separately in Seurat V5.
Then, I wonder where the data corresponding to var.features is stored in Seurat V5.

thank you

[mluciarr]

Hi @Dooo0k.
I got the same issue and I'm struggling to create the var.feature variable inside the object.
Did you eventually get a solution for that?
Or I'd really appreciate it if someone could help us.
Thanks a lot.

Lucia

[mluciarr]

I think the var.features in Seurat v5 is in SeuratObj@assays$RNA@meta.data$var.features
but I don't know how to take it out of the metadata compartment.

[Dooo0k]

Hi, @mluciarr
Thank you for the reply.

I was also unsure if 'scale.data' was considered a Variable features. But as far as I know, the 'ScaleData' function is usually used for genes that were selected in the 'Find variable features' step.

I think you can extract genes from the 'obj@assays$RNA@features@.Data' command by filtering for those with a 'TRUE' value for 'scale.data'.

[Dooo0k]

Furthermore, if you computed variable genes during PCA calculation, you can review the list of genes specified for PCA calculation through 'obj@reductions[["pca"]]@feature.loadings'.

If my understanding is incorrect, please provide feedback :D

[apal6]

Hi, I would like to follow up on this thread. I have the same issue. I encountered the error when I tried to project my data on a referEnce data (ProjectTil package). Error:
Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in as.vector(x): no slot of name "var.features" for this object of class "Assay5"
Would appreciate if someone could help?
Thank you in advance!

[amrita-singhs]

Haven't managed to find the slot in the object yet, but I'm using "VariableFeatures(object)" to access the list. Hope this helps someone