CMS subtype identification in Single cell data

Question

[David_emir]

Hi All,

Is it possible to identify CMS subtypes for Single-cell data (Seurat object)? I am having ~ 50000 single cells data and using Seurat for the analysis. I am interested in CMS subtyping, is it possible to use CMScaller on single-cell and if yes how can I used Seurat object (counts) as an input.

CMScaller

thanks for your help,

Regards, Dave

Answer 1

[jared.andrews07]

The vignette says it only need an expression matrix, so presumably yes, it will run on single cell data. On the other hand, I don't know anything about the tool or methods it uses, so underlying assumptions may be violated, which means it may not necessarily work.

It seems to want raw counts, and those are easy enough to get from Seurat via:

GetAssayData(object = pbmc, slot = "counts", assay = "RNA")

Their cheatsheet page has many common and useful Seurat functions and commands.