Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
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2.3 years ago
jrleary ▴ 190

I'm converting a SingleCellExperiment object to a Seurat object, and I'd like to be able to regress out the effect of % mitochondrial DNA when running SCTransform for normalization & detection of highly variable genes. However, running as.Seurat does not add the necessary nCount_RNA or nFeature_RNA metadata to the new Seurat object. Is there a non-exported function in Seurat that I could use to add this information?

scRNA-seq Seurat R • 3.2k views
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As quickly as I asked this, I figured it out. The hidden function CalcN performs this:

nCount = colSums(x = object, slot = "counts")  # nCount_RNA
nFeature = colSums(x = GetAssayData(object = object, slot = "counts") > 0)  # nFeatureRNA
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