Trouble using getBM with ecaballus_gene_ensembl
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@stephenwilliams-15198
Last seen 5.6 years ago

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)
[1] 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. 

biomart biomartr • 869 views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States

Does this help?

> getBM(attributes = c('entrezgene','hgnc_symbol', 'hgnc_id','ensembl_gene_id','external_gene_name'), filters = 'ensembl_gene_id', values = 'ENSECAG00000020530', mart = horse)
  entrezgene hgnc_symbol hgnc_id    ensembl_gene_id external_gene_name
1  100050870          NA      NA ENSECAG00000020530               RAI1
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Yes! This helps a lot. I didn't know about "external_gene_name".

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