I'm having trouble querying biomart using the biomaRt package for a non human species. for example, this works
library('biomaRt') mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") getBM(attributes = c('entrezgene','hgnc_symbol', 'ensembl_gene_id'), filters = 'hgnc_symbol', values = 'RAI1', mart = mart)
entrezgene hgnc_symbol ensembl_gene_id 1 10743 RAI1 ENSG00000108557
However when using the ecaballus_gene_ensembl mart the same thing does not work
library('biomaRt') horse = useMart("ensembl", dataset = "ecaballus_gene_ensembl") getBM(attributes = c('entrezgene','hgnc_symbol', 'ensembl_gene_id''), filters = 'hgnc_symbol', values = 'Rai1', mart = horse)
 entrezgene hgnc_symbol ensembl_gene_id <0 rows> (or 0-length row.names)
I have confirmed that this gene does exist in horse and that all the fields and filters do as well (confirmed using
listFilters(horse)) so I'm very confused. Any help would be greatly appreciated.