scMEGA icon indicating copy to clipboard operation
scMEGA copied to clipboard

problem with SelectTFs

Open Dalhte opened this issue 11 months ago • 5 comments

Hello there I'm tryingto run ScMega on 10X multiome RNA+ATAC data obtained in Rats tissus. When I run the : res <- SelectTFs(object = objG, tf.assay = "chromvar", rna.assay = "RNA", atac.assay = "ATAC", trajectory.name = "Trajectory", return.heatmap = TRUE, cor.cutoff = 0.1) I get Avis : No layers found matching search pattern provided Error in GetAssayData(): ! No layers are found Here are the backtrace : Backtrace: ▆

  1. └─scMEGA::SelectTFs(...)
  2. ├─base::suppressMessages(...)
  3. │ └─base::withCallingHandlers(...)
  4. └─scMEGA::GetTrajectory(...)
  5. ├─SeuratObject::GetAssayData(object, assay = assay, slot = slot)
    
  6. └─SeuratObject:::GetAssayData.Seurat(object, assay = assay, slot = slot)
    
  7.   ├─SeuratObject::GetAssayData(object = object[[assay]], layer = layer)
    
  8.   └─SeuratObject:::GetAssayData.StdAssay(object = object[[assay]], layer = layer)
    
  9.     └─rlang::abort("No layers are found")
    

Can you help me, please ? Is it because I'm working with the rat genome? Or is it something else entirely? Best David

Dalhte avatar Jul 26 '23 12:07 Dalhte