[R] How to create a chromosome location map by locus ID

[Sake]

Neil Shephard wrote:
> 
> 
> 
> 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
> 
> 
> 

I'm well known with all the tools on the internet which allow you to find
the position of genes on a chromosome. The only thing is, none of them has
the function to upload a list of e.g. 300 genes. I have a list of over
expressed genes, and I want to know on which chromosome they are so I can
see if there is some kind of link between the genes and the position on a
chromosome. I already have made a list of the locus of each gene, but now I
want to make some sort of plot that allows me to visualise where the genes
are located. So the reason I don't use those webtools is because I have 300
genes and I'm not planning to search for each gene individual.
The lodplot package looks promising (already found it;-), but thanx
anyway!), but I did not yet figured out how to use it properly. I've not
found any tutorial or example data to test it.
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