Question: Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
gravatar for jrleary
4 months ago by
Lineberger Comprehensive Cancer Center
jrleary130 wrote:

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?

seurat R scrna-seq • 348 views
ADD COMMENTlink written 4 months ago by jrleary130

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
ADD REPLYlink written 4 months ago by jrleary130
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1476 users visited in the last hour