Run on a single Seurat object

[JulieBvs]

Hello,

First, thank you for developing this nice tool.

I'm wondering if it's possible to identify gene modules from a single Seurat object ?

Thank you

[mass-a]

Hello Julie,
yes it's possible to run GeneNMF on a single object. If you only want to apply NMF as a dimensionality reduction (e.g. instead of PCA), you can use the runNMF() function directly on your Seurat object; see an example here.

You can also do the meta-program discovery over multiple k values with the multiNMF() function on one sample, simply by making a list of one element. Something like:

seu.list <- list("myobj" = seu.obj)
geneNMF.programs <- multiNMF(seu.list, k=5:10)
geneNMF.metaprograms <- getMetaPrograms(geneNMF.programs)

I hope that helps,
-m