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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Error: Cannot find 'ATAC' in this Seurat object #1709

Closed KunFang93 closed 6 months ago

KunFang93 commented 6 months ago

Hi,

I am trying to get a subset of object with selected regions but I run into error: Error: Cannot find 'ATAC' in this Seurat object when I tried to subset the seurat object with 

TTs.hcs.atac.seu <- subset(TTs.cancer.atac.seu, features=HCS_peaks$region)

But when I check TTs.cancer.atac.seu, it did have ATAC assay 

An object of class Seurat 
517625 features across 16679 samples within 3 assays 
Active assay: ATAC (289335 features, 289335 variable features)
 2 other assays present: ACTIVITY, peaks
 4 dimensional reductions calculated: integrated_lsi, umap, lsi, umap.atac

I wondered if I did it in a wrong way and how I could solve this? Thank you so much!

Best, Kun

KunFang93 commented 6 months ago

I found that it results from the rownames of my peaks assay (HCS_peaks derived from) are not the same with my ATAC assay