Hi runner...
runner <[EMAIL PROTECTED]> 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:
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> Sent from the R help mailing list archive at Nabble.com.
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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