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Question: Trouble using getBM with ecaballus_gene_ensembl
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gravatar for stephen.williams
9 weeks ago by
stephen.williams10 wrote:

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. 

ADD COMMENTlink modified 9 weeks ago by James W. MacDonald46k • written 9 weeks ago by stephen.williams10
1
gravatar for James W. MacDonald
9 weeks ago by
United States
James W. MacDonald46k wrote:

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
ADD COMMENTlink written 9 weeks ago by James W. MacDonald46k

Yes! This helps a lot. I didn't know about "external_gene_name".

ADD REPLYlink written 9 weeks ago by stephen.williams10
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