Matrix from getMatrixFromProject

[AnjaliC4]

Hi @rcorces,

I was wondering whether both the GeneIntegrationMatrix and GeneScoreMatrix exported from ArchR using getMatrixFromProject() are raw or log2 normalized counts?

In addition, is there a way to export MAGIC imputed matrices?

Thanks very much!

[AnjaliC4]

Hi @rcorces, would really appreciate your input on this whenever you have a chance.

Thank you

[rcorces]

Sorry for the delay. Its not so straightforward. The GeneIntegrationMatrix undergoes normalization (via Seurat::NormalizeData()) and scaling (via Seurat::ScaleData()). GeneScoreMatrix the exact math depends on the parameters you pass to the function. But the output is neither raw or log2 normalized counts per se and typically there are weights applied etc.

regarding exporting imputed matrices - no that is not possible because those matrices arent stored. They are calculated on the fly via the imputeMatrix() function. You could, of course, use that function yourself to obtain them.