Pathway analysis of a seurat object with gage in R

Question

[mfro]

Dear community

I am new to the field of RNA single cell sequencing and I am having problems performing pathway enrichment analysis on a Seurat object. I was able to perform pathway analysis on my object with the Reactome GSA package (Griss J. ReactomeGSA, https://github.com/reactome/ReactomeGSA (2019)), but I would prefer using the GAGE R Bioconductor package as it will let me use kegg or GO gene sets.

However, I get this error:

Could you help me figure out, how I need to prepare the data for gage analysis? As I cannot find a tutorial on how to prepare a Seurat object for GAGE. Or would you say using the ReactomeGSA package is as good and reliable as GAGE?

Thank you in advance.

M

[jv]

according to the gage help information, the format of the input exprs should be an expression matrix or matrix-like data structure, with genes as rows and samples as columns.

Your Seurat object is not a matrix, but you can get your gene x cell matrix out of the Seurat object. I myself am new to working with scRNA-seq data and have been playing around with Seurat objects. I think one good option for accessing the counts matrix is:

# get raw counts
GetAssayData(seuratObject, slot = "counts")

# get SCTransformed counts
GetAssayData(seuratObject, slot = "data")

I also found this GitHub issue informative regarding the different assay slots https://github.com/satijalab/seurat/issues/3711