[BioC] How to plot gene on their chromosome?

[Simon Noël]

I am sorry.  Has I say, I am new to R and bioconductor.  I am still learning.

I will try this tomorow and I will write you back to tell you the result. 
Thank's you for your help.  Il it's working, I will only have to wory about my
problem with qc()...  Or at least for now.  The summer is really young;)
Selon Hervé Pagès <hpages at fhcrc.org>, 21.05.2009:

> Hi Simon,
>
> Not a good idea to start a new thread by replying to a different thread
> you started previously. Then it shows up under the previous thread even
> if you changed the subject.
>
> more below...
>
> Simon Noël wrote:
> > Hello every one.  I have a question.  I have a gene list in a .xls like
> >
> > probeID	Symbol
> > 1030431	ACSL1
> > 4610431	ACTG2
> > 4810575	ADAMTSL2
> > 1510750	ADH1C
> > 4060519	ADORA1
> > 5720523	ADRA2A
> > 2810482	AHNAK
> > 1260270	AIM2
> > 4180768	ALAS2
> > ...     ...
> >
> > I want to plote all of those genes on their chromosome.  How can I do this?
>
> So first you need to map each gene to its chromosome location.
>
> You can use one of the org.*.eg.db annotation packages for
> this (pick up the one for your organism):
>
>    http://bioconductor.org/packages/release/data/annotation/
>
> and use the SYMBOL2EG map to map your gene symbols to their corresponding
> Entrez IDs and then the CHRLOC map to map your Entrez IDs to their chromosome
> locations.
>
> Example:
>
>    library(org.Hs.eg.db)
>    mysymbols <- c("ACSL1", "ACTG2", "ADAMTSL2", "ADH1C",
>                   "ADORA1", "ADRA2A", "AHNAK", "AIM2", "ALAS2")
>    myEgIDs <- unlist(mget(mysymbols, org.Hs.egSYMBOL2EG))
>    mylocs <- unname(unlist(mget(myEgIDs, org.Hs.egCHRLOC)))
>
> One thing to be aware of is that those mappings are not necessarily
> one-to-one e.g. the same symbol can be associated with different genes:
>
>    > flat <- toTable(org.Hs.egSYMBOL2EG)
>    > names(flat)
>    [1] "gene_id" "symbol"
>    > any(duplicated(flat$gene_id))
>    [1] FALSE
>    > any(duplicated(flat$symbol))
>    [1] TRUE
>
> The same thing happens with the org.Hs.egCHRLOC map (I'm not sure
> why we have this though, may be others on the list can explain).
>
> Anyway this explains why 'mylocs' can have more elements than 'mysymbols'.
>
> Cheers,
> H.
>
> >
> > Simon Noël
> > VP Externe CADEUL
> > Association des étudiants et étudiantes en Biochimie, Bio-
> > informatique et Microbiologie de l'Université Laval
> > CdeC
> >
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>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>


Simon Noël
VP Externe CADEUL
Association des étudiants et étudiantes en Biochimie, Bio-
informatique et Microbiologie de l'Université Laval
CdeC