[BioC] how to map choromosome location to gene ID

[Steffen Durinck]

Hi Yan,


This is a query similar to the one described in the biomaRt vignette section 4.5

http://bioconductor.org/packages/2.8/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf

for you that query might look like this:

library(biomaRt)
ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl")
getBM(c("ensembl_gene_id","hgnc_symbol","start_position","end_position"),
filters = c("chromosome_name", "start","end"), values = list(16,
1100000, 1250000), mart = ensembl)

you'll get:

 ensembl_gene_id hgnc_symbol start_position end_position
1 ENSG00000162009       SSTR5        1122756      1131454
2 ENSG00000184471     C1QTNF8        1138226      1146244
3 ENSG00000196557     CACNA1H        1203241      1271771
4 ENSG00000181791                    1115299      1116349


Cheers,
Steffen

On Wed, May 25, 2011 at 7:23 AM, Yan Jiao <y.jiao at ucl.ac.uk> wrote:
> Dear all,
>
> I'm trying to use biomaRt to map the chromosome location to gene ID,( I got chromosome number, start position and stop position, and it's for human)
> May I ask the syntax of it?
>
> Many thanks
>
> YAn
>
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>
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