[BioC] Retrieving Upstream Sequences With biomaRt

[Peter Robinson]

On Tue, Feb 20, 2007 at 12:11:02PM -0000, Stephen Henderson wrote:
> The first code that you show doesn't work--for many reasons.
> 
> >library(biomaRt)
> >ens<-useMart("ensembl",dataset="hsapiens_gene_ensembl", mysql=TRUE)
> >entrez <- c("100","330")
> >gene <- getGene(id=entrez, type="entrezgene", mart=ens)
> >getSequence(chromosome = gene$chromosome, start = gene$start - 2000,
> end= >gene$end + 1000, mart=ens)
> 
> 
> 1. gene$start and gene$end don't exist.
> 2. seqType is not specified.
> 3. seqType can't be specified as the type you want.
> 
> 
> >However, when I try the following line:
> >gene <- getGene(id=entrez, type="entrezgene", mart=ens)
> 
> that appears to be a problem with your database installation as if you
> do it over the web (i.e. drop mysql=TRUE):
> 
> ens<-useMart("ensembl",dataset="hsapiens_gene_ensembl")
> entrez <- c("100","330")
> gene <- getGene(id=entrez, type="entrezgene", mart=ens)
> 
> it works fine.
> 
> >The examples in the vignette all seem to work. What is wrong here?
> Where is >the file mentioned in the error message supposed to live? 
> 

Hmm..., I take it that the API of biomaRt has changed quite a bit. I got the code from a previous message to this list (I think), but perhaps it is easier to ask how to do things properly than to ask how to fix the code. Is there a way of retrieving upstream sequences with biomaRt?

Thanks, Peter


> 
> 
> Stephen Henderson
> Wolfson Inst. for Biomedical Research
> Cruciform Bldg., Gower Street
> University College London
> United Kingdom, WC1E 6BT
> +44 (0)207 679 6827
> 
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