Hi Martin,

Thanks for brining this to my attention.
I am wondering:

(1) Should the location information only be specified
in a way using 'e'? Will sth like 1234567 work?

(2) While the result return the gene function, can it also include
the gene symbol?

(3) In case I want to look up genes of multiple chromosomal regions,
how easily can I do that if I supply with a table of regions such as:

chr      Start                End
1     2171559         245522847
1     77465510       82255496
2     1                   243018229
2     145329129     187974870
3     1                    59538720


Thank you and happy holiday!

Allen

On Dec 26, 2007 12:26 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Allen --
>
> Also the 'org.*' annotation packages provide organism-centric
> annotations. These packages have environment-like key-value structures
> that typically map Entrez identifiers to other information. The CHRLOC
> variables map Entrez ids to named integer vectors. Names on the vector
> are chromosome locations, values are the strand (+ or -) and base
> start position. Thus
>
> > library(annotate)
> > library(org.Hs.eg.db)
> >
> > filt <- function(eid) {
> +     loc <- abs(eid) # either strand
> +     any(names(eid)=="3" & loc>1e8 & loc<1.1e8)
> + }
> > found <- unlist(eapply(org.Hs.egCHRLOC, filt))
> > sum(found) # named genes found
> [1] 33
> >
> > eids <- ls(org.Hs.egCHRLOC[found]) # subset; extract entrez ids
> > head(lookUp(eids, "org.Hs.eg.db", "GENENAME")) # first 6
> $`214`
> [1] "activated leukocyte cell adhesion molecule"
>
> $`868`
> [1] "Cas-Br-M (murine) ecotropic retroviral transforming sequence b"
>
> $`961`
> [1] "CD47 molecule"
>
> $`1295`
> [1] "collagen, type VIII, alpha 1"
>
> $`6152`
> [1] "ribosomal protein L24"
>
> $`9666`
> [1] "zinc finger DAZ interacting protein 3"
>
> The annotation packages are from data sources taken from a snapshot of
> data sources (see org.Hs.eg_dbInfo()) that might differ from the data
> sources used for biomaRt; the merits of this include (a)
> reproduciblilty and (b) relative speed of computation (no internet
> download required).
>
> Martin
>
>
> toedling@ebi.ac.uk writes:
>
> > Hi Allen,
> >
> > have a look at the biomaRt package:
> > http://www.bioconductor.org/packages/2.2/bioc/html/biomaRt.html
> > and see the vignette section 4.5 Task 5.
> > You may want to select additional attributes returned, such as
> > "description" etc. Use the "listAttributes" function to obtain of list
> of
> > possible attributes.
> >
> > Best and Merry Christmas,
> > Joern
> >
> >> Dear list,
> >>
> >> I am wondering if I supply with chromosome information, start and end
> >> position
> >> of a region, can any Bioconductor package could return a list of genes
> >> with
> >> short descriptions within those regions?
> >>
> >> Thanks and Merry Christmas!
> >>
> >> Allen
> >>
> >>
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> 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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