Accessing raw data after normalization

[marypiper]

we should add a markdown? or some text about how we can specify whether to use raw counts or normalized. The following code will allow us to extract the raw counts after normalization:

RNA_raw_assay <- seurat_integrated@assays$RNA@counts

seurat_integrated[['RNA_raw']] <- CreateAssayObject(counts = RNA_raw_assay)

RNA_norm_assay <- seurat_integrated@assays$RNA@data

seurat_integrated[['RNA_norm']] <- CreateAssayObject(counts = RNA_norm_assay)

DefaultAssay(seurat_integrated) <- "RNA_norm"