Extracting normalized counts from RDS (Seurat) file
I was performing scRNAseq integration between multiple datasets using Seurat and Harmony on R. I did manage to integrate but now I need to extract the normalized counts data from RDS file (Seurat Object) to use that matrix in another analyses. Is there a sufficient way or plugin/command to carry out such extraction?
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Ming Tommy Tang
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uyeiveycdikcdukyoz •
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uyeiveycdikcdukyoz •
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The seurat documentation has a section dedicated to the object manipulations and interactions: Command cheat sheet
Note, that Harmony does not change the underlying counts. it correct batches in the PCA space.