reference.SCT.model doesn't include the model for "vars.to.regress"

satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

GNU General Public License v3.0

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reference.SCT.model doesn't include the model for "vars.to.regress" #106

Closed albert-ying closed 3 years ago

albert-ying commented 3 years ago

Hi, I'm wondering why the model stored in seurat_obj[["SCT"]]@SCTModel.list$model1 only includes the model for nUMI, but not variables in vars.to.regress?

In my case, I want to build the SCTModel that include variables to regress-out from a large reference dataset and apply the same model to other small batches of new cells (in some extreme case, one cell), without integrating them to reference dataset and update everything. Is this possible?

Thank you!

ChristophH commented 3 years ago

Please head over to the Seurat issue tracker and look for an answer there, since this is a question that is specific to Seurat.