how to merge a subset dataset back to master seurat object
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7 days ago
catherine ▴ 180

Hi

I have a large dataset that has 10 clusters (cell type 1, 2...9,X), and I subset one of the clusters (cell type X) to perform another rounds of clustering and identified 3 cell types (cell type 1,2,3) which is also shown in my large dataset (NOT new cell types).

Now, I want to merge my sub-cluster back to previous data with assigned cell types, what is the best way to do it? Should I use integration?

scRNA RNAseq • 117 views
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You don't need to integrate. Since the small dataset is a subset of the big one, you can iterate through the values in original@meta.data (e.g UMIs) and add the new values from the subset@meta.data. For example, I would use a combination of match and ifelse.

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7 days ago

Why would you need integration? You're just changing cell metadata if all you're doing is updating cell type labels. Seurat has a cheatsheet for command manipulations like this. I'd probably just grab the metadata table and use merge, then reassign the metadata to the Seurat object.

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