group by multiple metadata

Hi!

I want to run the pipeline for my data with multiple conditions. Eg. my data has like fibroblast, adipocytes, etc. but also treated vs. control. Where is the parameter to input an additional condition?

Heres my code so far:

test <- irGSEA.score(object = Ma_2023, assay = "SCT", 
                             slot = "data", seeds = 123, ncores = 1,
                             min.cells = 3, min.feature = 0,
                             custom = F, geneset = NULL, msigdb = T, 
                             species = "Homo sapiens", category = "H",  
                             subcategory = NULL, geneid = "symbol",
                             method = c("AUCell", "UCell", "singscore", 
                                        "ssgsea"),
                             aucell.MaxRank = NULL, ucell.MaxRank = NULL, 
                             kcdf = 'Gaussian')

result.dge <- irGSEA.integrate(object = test, 
                               group.by = "Author_Provided_Clusters_LVL1", # this is the cluster names
                               metadata = NULL, col.name = NULL,
                               method = c("AUCell","UCell","singscore",
                                          "ssgsea"))

chuiqin / irGSEA

group by multiple metadata #19