[BioC] Mapping chromosome and nucleotide position to gene name

[Steven McKinney]

Thanks Steve,

The thread ideas work beautifully.

Thanks also to Martin Morgan for his ideas.

Best

Steve McKinney


> -----Original Message-----
> From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com]
> Sent: Thursday, April 16, 2009 1:03 PM
> To: Steven McKinney
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Mapping chromosome and nucleotide position to gene
> name
> 
> 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/2144
5
> 
> 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
> 
>