Hi,

I am using biomaRt to convert mouse gene symbols to human and vice versa.

Here is the code:

library(biomaRt)
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")

convertMouseGeneList <- function(x, y){

  # convert mouse to human
  genesV1 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = x , 
                   mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T)
  print(genesV1)

  # convert human to mouse
  genesV2 = getLDS(attributes = c("hgnc_symbol"), filters = "hgnc_symbol", values = y , 
                   mart = human, attributesL = c("mgi_symbol"), martL = mouse, uniqueRows=T)      
  print(genesV2)
}

x <- 'Rpl18' # mouse gene
y <- 'RPL18' # human gene

convertMouseGeneList(x, y)

This returns a NULL dataframe. However, on MGI, they have mentioned that the human ortholog to Rpl18 is RPL18. How can I fix this? I have also submitted an issue on github regarding this, but I wasn't sure about the response rate there.

Thanks!

I don't think it's an issue of fixing anything. Except do note that you can't return two sets of results like that. Your function by definition will only ever return the genesV1 results, and will never return the genesV2 results. As an example:

> z <- function(x,y) {return(x); return(y)}
> z("x","y")
[1] "x"

Also

> human <- useMart("ensembl", "hsapiens_gene_ensembl")
> mouse <- useMart("ensembl", "mmusculus_gene_ensembl")
> getLDS("mgi_symbol","mgi_symbol", "Rpl18", mouse, "hgnc_symbol", martL = human) 
[1] MGI.symbol  HGNC.symbol
<0 rows> (or 0-length row.names)
> getLDS("hgnc_symbol","hgnc_symbol","RPL18", human, "mgi_symbol", martL = mouse)
[1] HGNC.symbol MGI.symbol 
<0 rows> (or 0-length row.names)
## now for something that does map at the Biomart
> getLDS("hgnc_symbol","hgnc_symbol","TP53", human, "mgi_symbol", martL = mouse)
  HGNC.symbol MGI.symbol
1        TP53      Trp53
> getLDS("mgi_symbol","mgi_symbol", "Trp53", mouse, "hgnc_symbol", martL = human) 
  MGI.symbol HGNC.symbol
1      Trp53        TP53