try this

biocLite('Mus.musculus')
require(Mus.musculus)
require(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- transcriptsBy(TxDb.Mmusculus.UCSC.mm9.knownGene, 'gene')
egid <- names(txdb)
name <- unlist(mget(egid, org.Mm.egSYMBOL, ifnotfound=NA))
length(name) == length(egid) ## TRUE, OK to use
esbl <- unlist(mget(egid, org.Mm.egENSEMBL, ifnotfound=NA))
length(esbl) == length(egid) ## FALSE, do not use

probes <- GRanges(seq="chr17",
                  IRanges(start=31245606, width=1),
                  strand='*')
genome(probes) <- 'mm9' ## prevents some stoopid mistakes

geneBodyProbes <- findOverlaps(probes, txdb)
geneBodyProbes
## Hits of length 1
## queryLength: 1
## subjectLength: 21761
##   queryHits subjectHits
##    <integer>   <integer>
##     1         1        1641
##
name[subjectHits(geneBodyProbes)]
##   11307  # egid
## "Abcg1"  # name
##
org.Mm.egCHRLOC[['11307']]
##       17
## 31057694
##
org.Mm.egENSEMBL[['11307']]
## [1] "ENSMUSG00000024030"

promotersByGene <- flank(txdb, 1500) # or however many bases you want
promotersByGene <- flank(promotersByGene, 200, FALSE) # a little extra
promoterProbes <- findOverlaps(probes, promotersByGene)
promoterProbes
## Hits of length 0
## queryLength: 1
## subjectLength: 21761
##
## read the GRanges and GenomicFeatures vignettes for more




On Thu, Nov 8, 2012 at 7:28 AM, José Luis Lavín <jluis.lavin@unavarra.es>wrote:

> Dear James,
>
> To answer your questions swiftly, the features are methylation sites
> (that's why I only have a coordinate instead of having a Start/End pair) in
> mouse (mm9) genome and I have a list of those in the following format:
>
> chr17.31246506
>
> How could I read the list so that I can input the "chr" and the
> "coordinate" parameters into the expression you recommended?
>
> x <- GRanges(seq = "chr17", IRanges(start = 31245606, width = 1))
>
> I 'm lookin forward to obtain a table where my "coordinate-based Id"
> appears in a column, and the gene_name and if possible, the  Entrez/Ensembl
> Ids in two other columns :
>
> Coordinate Gene_name  Entrez_ID  Ensembl_ID
>
> Is it easy to do this in R?
>
> I'm still really new to R and I lack many concepts you may consider
> basic... I'm awfully sorry
>
> Best
>
> JL
>
> 2012/11/8 James W. MacDonald <jmacdon@uw.edu>
>
> > Hi Jose,
> >
> >
> > On 11/8/2012 8:19 AM, José Luis Lavín wrote:
> >
> >> Dear Bioconductor list,
> >>
> >> I write you this email asking for a Bioconductor module that allows me
> to
> >> annotate genomic coordinates and get different GeneIds.
> >> I'll show you an example of what I'm referring to:
> >>
> >> I have this data:
> >> Chromosome  coordinate
> >> chr17              31246506
> >>
> >
> > It depends on what that coordinate is. Is it the start of a transcript? A
> > SNP? Do you really just have a single coordinate, or do you have a range?
> > What species are we talking about here?
> >
> > Depending on what your data are, you might want to use either one of the
> > TxDb packages, or a SNPlocs package. There really isn't much to go on
> here.
> > If I assume this is a coordinate that one might think is within an exon,
> > and if I further assume you are working with H. sapiens, I could suggest
> > something like
> >
> > library(TxDb.Hsapiens.UCSC.**hg19.knownGene)
> > ex <- exonsBy(TxDb.Hsapiens.UCSC.**hg19.knownGene, "gene")
> >
> > x <- GRanges(seq = "chr17", IRanges(start = 31245606, width = 1))
> >
> > ex[ex %in% x]
> >
> > or maybe more appropriately
> >
> > names(ex)[ex %in% x]
> >
> > which will give you the Gene ID, and you can go from there using the
> > org.Hs.eg.db package.
> >
> > If however, your coordinate isn't in an exon, but might be in a UTR, you
> > can look at ?exonsBy to see what other sequences you can extract to
> compare
> > with.
> >
> > If these are SNPs, then you can look at the help pages for the relevant
> > SNPlocs package.
> >
> > Best,
> >
> > Jim
> >
> >
> >
> >> which can also be written this way by the program that yielded the
> result:
> >> chr17.31246506
> >>
> >> And I need to convert this data into a gene name and known gene Ids,
> such
> >> as:
> >>
> >> Gene name  Entrez_ID  Ensembl_ID
> >>
> >> Tff3 NM_011575 20050
> >> Can you please advice me about a module able to perform this ID
> conversion
> >> using a list of  "chr17.31246506" type coordinates as input?
> >>
> >> Thanks in advance
> >>
> >> With best wishes
> >>
> >>
> >>
> >> ______________________________**_________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<
> https://stat.ethz.ch/mailman/listinfo/bioconductor>
> >> Search the archives: http://news.gmane.org/gmane.**
> >> science.biology.informatics.**conductor<
> http://news.gmane.org/gmane.science.biology.informatics.conductor>
> >>
> >
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > University of Washington
> > Environmental and Occupational Health Sciences
> > 4225 Roosevelt Way NE, # 100
> > Seattle WA 98105-6099
> >
> >
>
>
> --
> --
> Dr. José Luis Lavín Trueba
>
> Dpto. de Producción Agraria
> Grupo de Genética y Microbiología
> Universidad Pública de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
>
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>
>
> _______________________________________________
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>
>


-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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