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carmonalab / ProjecTILs

Interpretation of cell states using reference single-cell maps
GNU General Public License v3.0
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customized reference TIL map? #10

Closed gt7901b closed 3 years ago

gt7901b commented 3 years ago

Hi,

Is there a way to make customized reference TIL map?

thanks

gt7901b commented 3 years ago

I followed this tutorial https://carmonalab.github.io/ProjecTILs/build_ref_atlas.html to build customized reference. I don't have integrated assay, so I just used which.assay="RNA"

but when I run make.projection, it asked for integrated assay, how to solve this?

thanks

query.projected <- make.projection(seurat.obj, ref = myref, human.ortho=TRUE)

Error in DefaultAssay<-.Seurat(*tmp*, value = "integrated"): Cannot find assay integrated

Traceback:

  1. make.projection(seurat.obj, ref = myref, human.ortho = TRUE)
  2. DefaultAssay<-(*tmp*, value = "integrated")
  3. DefaultAssay<-.Seurat(*tmp*, value = "integrated")
  4. stop("Cannot find assay ", value)
mass-a commented 3 years ago

You are correct, the algorithm assumes the "integrated" assay is present for the reference atlas.

If your custom reference does not have this assay, you could simply make a copy of the 'RNA' assay:

myref@assays$integrated <- myref@assays$RNA

and then follow the customized atlas tutorial as you did.