[BioC] Mapping chromosome and nucleotide position to gene name

[Steven McKinney]

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?

So far all my searches show how to do this with e.g. Affymetrix data contained
in various expressionSet etc. objects, but I need to do this from this basic
data state.

Any suggestions appreciated



Steven McKinney, Ph.D.

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada