[BioC] How to plot gene on their chromosome?

[Simon Noël]

I have try your procedure and every thing is loking fine for now.  What's the
netx step to plot my genes on their chromosomes?

Selon Simon Noël <simon.noel.2 at ulaval.ca>, 21.05.2009:

> 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
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > --
> > 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


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