Ensembl site unresponsive when using creat_cellphonedb_file() function

[pandaqiuqiu]

When I use the creat_cellphonedb_file() function to generate the input files for CellPhoneDB, I encountered the following error:

creat_cellphonedb_file(sce, Sample)

Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying asia mirror
Error: biomaRt has encountered an unexpected server error.
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

Additionally, I am curious why this process needs to call biomaRt. Any response will be appreciated.

[HaojiaWu]

Hi @pandaqiuqiu
The earlier version of CellPhoneDB used a ligand-receptor pair database derived from human genes. Therefore, I need to convert mouse genes to their orthologous human genes, which is why I am using biomaRt. I've tested biomaRt on my server, and it works fine with version 2.60.0. You can use the same version to see if it works for you.
I will add an argument to the function later to allow users to specify the species. For a quick fix, you can modify the source code of the function. The source code is very short (see below). If your Seurat object is from a human sample, you can omit the biomaRt lines.

creat_cellphonedb_file <- function(seu_obj, group){
  counts <- as.data.frame(
    as.matrix(
      seu_obj@assays$RNA@data)
  )
  mouse_genes<-rownames(counts)
  human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "https://dec2021.archive.ensembl.org/") 
  mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")
  genesV2 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", 
                   values = mouse_genes , mart = mouse, attributesL = c("hgnc_symbol",'ensembl_gene_id'), 
                   martL = human, uniqueRows=F)
  genesV2$Gene.stable.ID<-as.character(genesV2$Gene.stable.ID)
  genesV2$MGI.symbol<-as.character(genesV2$MGI.symbol)
  genesV2<-genesV2[!duplicated(genesV2$Gene.stable.ID),]
  genesV2<-genesV2[!duplicated(genesV2$MGI.symbol),]
  counts<-counts[genesV2$MGI.symbol,]
  rownames(counts)<-genesV2$Gene.stable.ID
  metadata <- data.frame(Cell = colnames(counts),
                         cell_type = as.character(seu_obj@active.ident)
  )
  metadata$Cell<-gsub('\\-','\\.',metadata$Cell)
  counts<-na.omit(counts)
  counts$Gene<-rownames(counts)
  counts<-counts[,c(ncol(counts), 1:(ncol(counts)-1))]
  colnames(counts)<-gsub('\\-','\\.',colnames(counts))
  
  write.table(counts,
              file =paste0(group, '_counts.txt'),
              quote = F,
              col.names = T,
              row.names = F,
              sep = '\t')
  
  write.table(metadata,
              file = paste0(group, '_metadata.txt'),
              quote = F,
              col.names = T,
              row.names = F,
              sep = '\t')
  
}