list genes w/n a genomic fragment

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.

-----
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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.

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______________________________________________
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793