I have a bunch of swiss prot IDs that I want to convert to hgnc symbols. To do that I am using biomart and for most genes, it works. But for a small minority, it cannot find a corresponding symbol for a given ID even though web interface of biomart successfully handles the conversion.
I added an example for a single gene below.
humanMart = useMart("ensembl", dataset="hsapiens_gene_ensembl") humanTrans = getBM(attributes = c('uniprot_swissprot','hgnc_symbol','ensembl_gene_id'), # just take the human ones. just in case... filters = 'uniprot_swissprot', values = 'Q9Y2R4', mart = humanMart) humanTrans[humanTrans$uniprot_swissprot %in% 'Q9Y2R4',] uniprot_swissprot hgnc_symbol ensembl_gene_id 15191 Q9Y2R4 ENSG00000277594
Thanks. In that case do you know what is the data for biomart's ID converter web interface is coming from?