R help - Jan 2009 - How to create a chromosome location map by locus ID

Hi,

I'm trying to make a chromosomal map in R by using the locus. I have a list
of genes and their locus, and I want to visualise that so you can see if
there are multiple genes on a specific place on a chromosome. A example of
what I more or less want is below:
http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG 
The genes and locus are here:
http://www.nabble.com/file/p21474206/genlocus.csv genlocus.csv 
I've tried some things, but nothing worked like I would like it to see.
Maybe there is some kind of package that does this for you, but I did not
find it yet.
Thanx

Sake
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Hi Sake:
If you do not find an answer within the list, MapChart will probably do 
what you want (without the fancy chromosomal bands, though). You can 
find it at

http://www.biometris.wur.nl/uk/Software/MapChart/

Hope this helps

Sake escribi?:
> Hi,
>
> I'm trying to make a chromosomal map in R by using the locus. I have a
list
> of genes and their locus, and I want to visualise that so you can see if
> there are multiple genes on a specific place on a chromosome. A example of
> what I more or less want is below:
> http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG 
> The genes and locus are here:
> http://www.nabble.com/file/p21474206/genlocus.csv genlocus.csv 
> I've tried some things, but nothing worked like I would like it to see.
> Maybe there is some kind of package that does this for you, but I did not
> find it yet.
> Thanx
>
> Sake
>   
-- 

*Pablo G Goicoechea*

Bioteknolog?a Saila / /Dpto Biotecnolog?a/

NEIKER-Tecnalia

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01080 Vitoria-Gasteiz (SPAIN)

Phone: +34 902 540 546 Fax: +34 902 540 547

pgoikoetxea at neiker.net <mailto:pgoikoetxea at neiker.net>

Sake wrote:
> 
> Hi,
> 
> I'm trying to make a chromosomal map in R by using the locus. I have a
> list of genes and their locus, and I want to visualise that so you can see
> if there are multiple genes on a specific place on a chromosome. A example
> of what I more or less want is below:
>  http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG 
> The genes and locus are here:
> http://www.nabble.com/file/p21474206/genlocus.csv genlocus.csv 
> I've tried some things, but nothing worked like I would like it to see.
> Maybe there is some kind of package that does this for you, but I did not
> find it yet.
> Thanx
> 
> Sake
> 
Whats wrong with things like the HapMap Genome Browser that allows you to
zoom in and out and to produce customised annotations of chromosomal regions
at varying resolutions (see http://www.hapmap.org/)?  Of course I'm assuming
that you are looking at human chromosomes ;-) If not
then perhaps the UCSC Genome Browser may be of use as it has a large number
genomes you can browse (see http://genome.ucsc.edu/cgi-bin/hgGateway ).

If you really want to do this in R You might get some mileage out of the
lodplot package which can draw ideograms (which is what a schematic of a
choromsome with bandings from different stainings is called), although the
dataset available for it is again for human chromosomes (see
http://cran.r-project.org/web/packages/lodplot/index.html ).

Perhaps worth checking out the Genetics Task View too thats linked from
CRAN.

Neil


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