[BioC] Mapping chromosome and nucleotide position to gene name

[Steve Lianoglou]

Hi,

On Apr 16, 2009, at 3:51 PM, Steven McKinney wrote:

> Hi all,
>
>> From the output of a custom HMM routine,
> I have data showing chromosome number and nucleotide position,
> but no associated gene name or database identifier.  e.g.
>> logRiList[[1]][1:10,]
>   chromosome position    end    logR state
> 1           1    10004  10004  0.7627     3
> 2           1    46844  46844 -0.1648     3
> 3           1    59415  59415  0.1096     3
> 4           1    97215  97215  0.5914     3
> 5           1   224176 224176  0.6766     3
> 6           1   227744 227744  0.7047     3
> 7           1   311662 311662  0.4185     3
> 8           1   314893 314893  0.9843     3
> 9           1   318309 318309  0.2642     3
> 10          1   320085 320085  0.7877     3
>
> How can I map this data to RefSeq Accession number or EntrezGene ID  
> etc. so
> I can get the name of the gene associated with a given chromosome  
> and nucleotide
> position?

I'm not sure if this is optimal, but it's quite similar to what the  
poster was trying to do in this thread:

http://thread.gmane.org/gmane.science.biology.informatics.conductor/21445

See Martin Morgan's response for an idea of how to take a crack at it  
using your organism's GTF/GFF and the IRanges package.

HTH,

-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos