Zhu, Lihua (Julie | 26 Feb 14:21 2013

Re: Finding closest gene to chromosomal position (non-human or mouse)

Molly,

You might want to try annotatePeakInBatch in ChIPpeakAnno package with
parameter output="both".

Best regards,

Julie

On 2/25/13 4:35 PM, "Molly Hanlon" <hanlonmt@...> wrote:

> Hi list,
> 
> I've been using R for some time, but am new to bioconductor/biomaRt. Please
> pardon that.
> 
> I have a list of a couple thousand SNPs and I'm looking for the closest
> gene to each of them.  Looking just within the gene, I only get a result
> for about a third of them, so I obviously need something a bit more robust.
>  Searching the archives, I've found mention of the findClosestGene in ACME,
> however, I work in rice, so this isn't much help. Ideally, I'd like to
> enter a position, say "9:12344567" and get an output that it lies 1234 bp
> upstream from Loc_OsXXXXXX.
> 
> I've also seen suggestions that include getting a data frame of all the
> gene positions  and then using findOverlap with my frame, though I'm not
> sure this would work because I have no strand information for my query and
> they're single base pairs, thus without a range.
> 
> Feel free to correct my assumptions, but any additional help you can
> provide would be wonderful.
> 
> Many thanks,
> Molly
> 
> [[alternative HTML version deleted]]
> 
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