[Seurat5]: SCTModel.list contains only a subset of feature attributes after calling SCTransform

[Gilquin]

Running SCTransform on a Seurat v5 object (Assay5 class for RNA assay) will return an SCT assay where any of the SCTModel may miss some feature.attributes if the number of cells is less than the argument ncells (default to 5000). In this case, the following subset of feature.attributes is lost: detection_rate, gmean and variance.

The culprit is a call to the function SCTModel_to_vst which skips the fields detection_rate, gmean and variance.

This removes the possibility of using the function VariableFeaturePlot on the newly created SCT assay (which calls HVFInfo.SCTAssay which itself searches for gmean and variance, see the corresponding line).

Is this intended or not? If not, a possible solution would be to add the following line:

vst_out.reference$gene_attr <- local.reference.SCT.model@feature.attributes

there, in the SCTransform.StdAssay function body.

Here is a reproducible example:

options(Seurat.object.assay.version = "v5")

# Load data
Sobject <- Seurat::UpdateSeuratObject(pbmc3k.SeuratData::pbmc3k)

# Create Seurat v5 object
SobjectV5 <- SeuratObject::CreateSeuratObject(
  counts = SeuratObject::CreateAssay5Object(counts = Sobject[["RNA"]]@counts),
  assay = "RNA",
  meta.data = Sobject@meta.data,
  project = Sobject@project.name
)

# SCT normalization
SobjectV5 <- Seurat::PercentageFeatureSet(SobjectV5, pattern = "^MT-", col.name = "percent.mt")
SobjectV5 <- Seurat::SCTransform(
  SobjectV5,
  vst.flavor = "v2",
  vars.to.regress = "percent.mt",
  seed.use = 404,
  ncells = 2000
  )

# Check the missing columns
str(SobjectV5[["SCT"]]@SCTModel.list$model1@feature.attributes)

Note that running the example with ncells = 5000 returns the full set of feature.attributes as an "edge" case.

[saketkc]

Thank you @Gilquin for a reproducible example. We should support it and will release a fix soon.

[saketkc]

Hi @Gilquin, thanks for the reproducible example. This has been fixed internally and will be in the official Seurat V5 release.