Hi all,

I am currently trying to map human genes to mouse orthologs using biomaRt and the getLDS. However, I encounter the following error:

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

This is the code that I used:

library(biomaRt)
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host="https://www.ensembl.org")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", host="https://www.ensembl.org")

res <- getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"),
              filters = "hgnc_symbol", values = "TP53", mart = human,
              attributesL = c("chromosome_name","start_position"), martL = mouse)

I am using R version 4.2.0 and biomaRt version 2.52.0. Essentially it is the same issue that was described here. In this post however, I did not really find a solution, because changing mirrors didn't work.

Any idea what else I can try?

No idea what the issue with biomaRt might be, but there are other ways to do this. As an example:

## load stuff
> library(Homo.sapiens)
> library(TxDb.Hsapiens.UCSC.hg38.refGene)
> TxDb(Homo.sapiens) <- TxDb.Hsapiens.UCSC.hg38.refGene
> library(Mus.musculus)
> library(Orthology.eg.db)
## cob together a function
mapFun <- function(genes) {
    humeg <- mapIds(org.Hs.eg.db, genes, "ENTREZID","SYMBOL")
    mouseg <- mapIds(Orthology.eg.db, humeg, "Mus.musculus","Homo.sapiens")
    humdat <- select(Homo.sapiens, humeg, c("SYMBOL","CDSCHROM","CDSSTART","CDSEND", "CDSSTRAND"), "GENEID")
    mousedat <- select(Mus.musculus, mouseg,  c("SYMBOL","CDSCHROM","CDSSTART","CDSEND", "CDSSTRAND"), "GENEID")
    return(list(humdat = humdat, mousedat = mousedat))
}

## Test drive
> mapFun("TP53")
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
$humdat
   GENEID CDSCHROM CDSSTRAND CDSSTART  CDSEND SYMBOL
1    7157    chr17         -  7675053 7675134   TP53
2    7157    chr17         -  7674859 7674971   TP53
3    7157    chr17         -  7674181 7674290   TP53
4    7157    chr17         -  7673701 7673837   TP53
5    7157    chr17         -  7673535 7673608   TP53
6    7157    chr17         -  7670609 7670715   TP53
7    7157    chr17         -  7669609 7669690   TP53
8    7157    chr17         -  7673307 7673339   TP53
9    7157    chr17         -  7673219 7673266   TP53
10   7157    chr17         -  7675053 7675215   TP53
11   7157    chr17         -  7675994 7676251   TP53
12   7157    chr17         -  7675053 7675236   TP53
13   7157    chr17         -  7676521 7676594   TP53
14   7157    chr17         -  7676382 7676403   TP53
15   7157    chr17         -  7675994 7676272   TP53

$mousedat
   GENEID CDSCHROM CDSSTRAND CDSSTART   CDSEND SYMBOL
1   22059    chr11         + 69586891 69586973  Trp53
2   22059    chr11         + 69587257 69587278  Trp53
3   22059    chr11         + 69587372 69587632  Trp53
4   22059    chr11         + 69588364 69588547  Trp53
5   22059    chr11         + 69588626 69588738  Trp53
6   22059    chr11         + 69589141 69589250  Trp53
7   22059    chr11         + 69589573 69589709  Trp53
8   22059    chr11         + 69589789 69589862  Trp53
9   22059    chr11         + 69590656 69590762  Trp53
10  22059    chr11         + 69591350 69591431  Trp53
11  22059    chr11         + 69591254 69591308  Trp53
12  22059    chr11         + 69586900 69586973  Trp53

But maybe you don't really want the TSS, but instead the general region of the gene.

naiveFun <- function(genes) {
    humeg <- mapIds(org.Hs.eg.db, genes, "ENTREZID","SYMBOL")
    mouseg <- as.character(mapIds(Orthology.eg.db, humeg, "Mus.musculus","Homo.sapiens"))
    mousesymb <- mapIds(org.Mm.eg.db, mouseg, "SYMBOL", "ENTREZID")
    humdat <- as(suppressMessages(genes(Homo.sapiens)[humeg]), "data.frame")
    mousedat <- as(suppressMessages(genes(Mus.musculus)[mouseg]), "data.frame")
    data.frame(rbind(humdat, mousedat), SYMBOL = c(genes, mousesymb), SPECIES = c("Homo sapiens","Mus musculus"))
}

> naiveFun("TP53")
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
      seqnames    start      end width strand GENEID SYMBOL      SPECIES
7157     chr17  7668402  7687550 19149      -   7157   TP53 Homo sapiens
22059    chr11 69580359 69591873 11515      +  22059  Trp53 Mus musculus