Error in RenameGenesSeurat

[JH-42]

Hi, thank you for the wonderful function!
I met the same problem as jenellewallace.

> HGNC.updated <- HGNChelper::checkGeneSymbols(rownames(Tcells), unmapped.as.na = FALSE, map = NULL, species = "human")

>  Tcells@version
[1] ‘5.0.1’
> Tcells<-Seurat.utils::RenameGenesSeurat(obj = Tcells,newnames = HGNC.updated$Suggested.Symbol,assay = "RNA",slots=c("data","counts"))
RenameGenesSeurat, assay: RNA
Warning in Seurat.utils::RenameGenesSeurat(obj = Tcells, newnames = HGNC.updated$Suggested.Symbol,  :
  Run this before integration and downstream processing. It only attempts to change
          @counts, @data, and @meta.features in obj@assays$YOUR_ASSAY.
[1] "Present:  counts data scale.data"
[1] "Replaced:  counts data"
[1] "counts"
counts
Error in rownames(assayobj@features@.Data) :
  no slot of name "features" for this object of class "Assay"

[vertesy]

Hey JH,

thanks and sorry for the trouble. Very busy these days, try to address it next week.

//A

[JH-42]

Thanks for your help. I solved my problem using other methods. I'm writing my solution here in case anyone needs it in the future.

library(nichenetr)
library(Seurat)
exp_mtx <- as.matrix(Tcells1@assays$RNA@data)
con_df <- data.frame(mouse = rownames(exp_mtx),
                     hum_orig = convert_mouse_to_human_symbols(rownames(exp_mtx)),
                     stringsAsFactors = F)

con_df <- con_df[!is.na(con_df$hum_orig),,F]
exp_mtx <- exp_mtx[con_df$mouse,]
rownames(exp_mtx) <- con_df$hum_orig
human_SO <- CreateSeuratObject(counts = exp_mtx, meta.data = Tcells1@meta.data )

[gabrielascui]

Hi, I'm getting the same error, is there a way to do this with generating a new matrix with the new names?

I'm using a dataset I downloaded as an .rds file from https://cellxgene.cziscience.com/datasets

tabula.sapiens.ref <- readRDS(path.ref) # single cell database for large intestine human
tabula.sapiens.ref <- UpdateSeuratObject(tabula.sapiens.ref)

tabula.sapiens.ref <- RenameGenesSeurat(tabula.sapiens.ref, newnames = as.character(tabula.sapiens.ref@[email protected]$feature_name))

I'm not sure were is the features slots being called by the function.