Error using `RunNICHES()`: "mutate has no applicable method for 'list' target objects"

[chengwanjie379]

Hi,I am currently working on a spatial transcriptomics analysis using NICHES packages in R. I encountered an error while running RunNICHES() that states:

Error in UseMethod("mutate"): "mutate" has no applicable method for 'list' target objects

Additionally, I received a warning message:

Warning: OmnipathR::import_ligrecextra_interactions is no longer functional.

Here’s the relevant portion of my code:

NICHE_output <- RunNICHES(object = UCEC, 
                          LR.database = "omnipath", 
                          species = "human", 
                          assay = "alra", 
                          position.x = 'x', 
                          position.y = 'y', 
                          k = 4, 
                          cell_types = "seurat_clusters", 
                          meta.data.to.map = c('orig.ident','seurat_clusters'), 
                          CellToCell = F, 
                          CellToSystem = F, 
                          SystemToCell = F, 
                          CellToCellSpatial = F, 
                          CellToNeighborhood = F, 
                          hoodToCell = T)

It seems that the function mutate is not correctly applied to a 'list' object, and the import_ligrecextra_interactions function from OmnipathR is deprecated.

Could you please advise on how to resolve this error? Specifically, I would like to know:

1. How to handle the mutate error in this context?
2. What is the recommended approach now that import_ligrecextra_interactions is deprecated?

Thank you in advance for your help!