Alternative to to.upper parameter Load10X_Spatial?

[samuel-marsh]

HI Seurat Team,

Wondering whether there might be better alternative to the to.upper parameter in Load10X_Spatial? The goal as stated in manual makes sense: Can be useful when analyses require comparisons between human and mouse gene names for example.

However, in practice converting all the gene names to upper case may give user the false impression that genes with same name are homologous when that is not always the case (and name mismatches etc depending on reference annotation version).

It's not really feasible to call biomaRt (especially with modifications for different reference annotation versions) from within function like this but wondering if either a note in the manual about gene equivalency or temporarily disabling the parameter might be better? Obviously up to you but I think could be easy for many to miss the subtleties.

Best,
Sam

[timoast]

Hi @samuel-marsh, this is a very good point. The parameter is there mainly to facilitate quick comparisons between human and mouse, but for an accurate comparison across species the actual homologs need to be used. We'll update the documentation to make this clear

[timoast]

This should now be updated on the develop branch

[samuel-marsh]

Hi @timoast ya totally makes sense. Wanted to raise the issue so Seurat team could decide best course of activation (documentation vs. alterative funtion, etc). Looks good to me!

Best,
Sam