[BioC] biomaRt: getting start and end locations of gene on chromosome

James W. MacDonald jmacdon at med.umich.edu
Mon Jul 6 21:39:59 CEST 2009

Hi Tim,

I would replace "with_entrezgene" with "entrezgene":

"entrezgene",entrezID, mart)
   hgnc_symbol chromosome_name start_position end_position
1        WNT1              12       47658503     47662746

I would also add entrezID to the attributes - it helps to know what 
things you didn't get, as well as things that map to the same ID more 
than once.



Tim Smith wrote:
> Hi,
> Given a set of entrez IDs, I wanted to know their start and end locations on the chromosome. I am using biomaRt, but get the following error:
> -------------------------------------------
>> entrezID = "7471" 
>> getBM(attributes = c('hgnc_symbol','chromosome_name','start_position',
> +       'end_position'),mart = ensembl, filters = 'with_entrezgene',
> +         values = entrezID)
> Error in getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position",  : 
>   biomaRt error:  with_entrezgene  is a boolean filter and needs a corresponding logical value of TRUE or FALSE to indicate if the query should retrieve all data that fulfill the boolean or alternatively that all data that not fulfill the requirement should be retrieved.
> -------------------------------------------
> I read the documentation and it said that this particular filter needs a boolean value (error statement says the same), but it didn't say how I was actually to set it. How do I go about doing this?
> thanks!
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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