R help - Jul 2008 - list genes w/n a genomic fragment

Hi, is there any package/function in Bioconductor that can do this: if given
the chromosome positions of a fragment, find out all genes within, and with
the information about which strand is the sense strand.  And vice versa.
Thanks a lot.

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So Mr.Anoymous, why don't you inquire on the Bioconductor list to find out
instead of here?

-- Bert Gunter

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
Behalf Of runner
Sent: Monday, July 07, 2008 8:59 PM
To: r-help at r-project.org
Subject: [R] list genes w/n a genomic fragment


Hi, is there any package/function in Bioconductor that can do this: if given
the chromosome positions of a fragment, find out all genes within, and with
the information about which strand is the sense strand.  And vice versa.
Thanks a lot.

-----
Appreciate your time & attention!
-- 
View this message in context:
http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.
html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Hi runner...

runner <sunnyside500 at gmail.com> writes:
> Hi, is there any package/function in Bioconductor that can do this:
As Bert says, this should be directed to the Bioconductor mailing
list. Let's have any follow-up conversation there. But...
> if given the chromosome positions of a fragment, find out all genes
> within, and with the information about which strand is the sense
> strand.
Organism-centric packages contain information about chromosome
locations of ENTREZ gene IDs, so...
> library(org.Mm.eg.db)
> tbl <- toTable(org.Mm.egCHRLOC)
> idx <- with(tbl,
+             Chromosome == 1 &
+             abs(start_location) > 10^7 &
+             abs(start_location) < 2*10^7)
> tbl[idx,]
      gene_id start_location Chromosome
1426    14048      -14159038          1
1709    14545       17135477          1
2745    17087       16678536          1
2961    17681      -14743428          1
3106    17978      -13129239          1
4066    19989      -16091378          1
...

the '-' indicates strand.
> And vice versa.
easy to look up the chromosome locations of an ENTREZ id, if that's
what you mean...
> mget("20671", org.Mm.egCHRLOC)
$`20671`
       1 
-4481008

or
> tbl[tbl$gene_id=="20671",]
     gene_id start_location Chromosome
4445   20671       -4481008          1

Martin
> Thanks a lot.
>
> -----
> Appreciate your time & attention!
> -- 
> View this message in context:
http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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