This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Splitting Seurat object by sample layers

Hello,

I have this seurat object:

An object of class Seurat 
16143 features across 29645 samples within 1 assay 
Active assay: RNA (16143 features, 2000 variable features)
5 layers present: counts.control, counts.treated, data.control, data.treated, scale.data
2 dimensional reductions calculated: pca, umap

I would like to split this by sample layer so I will have 2 separate Seurat objects, one of which such as:

An object of class Seurat 
15143 features across 19645 samples within 1 assay 
Active assay: RNA (16143 features, 2000 variable features)
3 layers present: counts.control (or named just "counts"), data.control, scale.data
2 dimensional reductions calculated: pca, umap

Do you know how to do that?

seurat
• 1,493 views • link
updated by Ram Ram • written by kilcdincer • kilcdincer

1 answer

You can do the following-

Idents(SeuratObj) <- "orig.ident"
control_set <- subset(SeuratObj, idents = c("counts.control","data.control"))

#for treated data, you can do the following-
treated_set <- subset(SeuratObj, idents = c("counts.treated","data.treated"))
• 0 views • link
updated by Ram Ram • written by bk11 • bk11

Log in to answer this question.

More posts like this