Error by using mouse_genes_to_human function

[kongjianyang]

If you meet problem by using mouse_genes_to_human like,

mouse_genes_to_human(tpm_data)
# Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www.ensembl.org:443] Operation timed out after 10001 milliseconds with 0 bytes received

you can create your own function by modify the original code:

my_mouse_genes_to_human <- function (gene_expression_matrix, mirror = "www") 
{
    gene.names.mouse <- rownames(gene_expression_matrix)
    gene_expression_matrix$gene_name <- gene.names.mouse
    
      # add host to 2021 version, otherwise may have bug
    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/")
    
    
    genes.retrieved <- getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", 
        values = gene.names.mouse, mart = mouse, attributesL = c("hgnc_symbol"), 
        martL = human, uniqueRows = T)
    
    
    newGenes.counts <- gene_expression_matrix %>% left_join(., 
        genes.retrieved, by = c(gene_name = "MGI.symbol")) %>% 
        dplyr::select(., -c("gene_name")) %>% dplyr::select(., c("HGNC.symbol", 
        everything())) %>% .[!(is.na(.$HGNC.symbol)), ]
    colnames(newGenes.counts)[1] <- "gene_name"
    newGenes.counts <- newGenes.counts[!(duplicated(newGenes.counts$gene_name)), 
        ] %>% as.data.frame(.)
    rownames(newGenes.counts) <- newGenes.counts$gene_name
    newGenes.counts <- dplyr::select(newGenes.counts, -c("gene_name"))
    fraction <- 100 * (nrow(newGenes.counts)/nrow(gene_expression_matrix)) %>% 
        round(., 1)
    message(paste0("ATTENTION: Only the ", fraction, "% of genes was maintained"))
    return(newGenes.counts)
}

then using

# mouse data, change to human gene ID
expression_matrix_humanGenes <- my_mouse_genes_to_human(gene_expression_matrix, mirror = "www")

This will solve your problem.

[Kiliankleemann]

Error: 'mouse_genes_to_human' is not an exported object from 'namespace:immunedeconv'