[BioC] Retrieving Upstream Sequences With biomaRt

[Stephen Henderson]

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? 



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

**********************************************************************
This email and any files transmitted with it are confidentia...{{dropped}}