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How to create a chromosome location map by locus ID

6 messages · Sake, Pablo G Goicoechea, Neil Shephard +1 more

Original
Sake
# 
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
# 
Sorry list, I guess I sent an html reply.

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?:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Neil Shephard
    

    

      
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Sake 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

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Sake
    

    

      
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Neil Shephard wrote:

            

      
      
      
    

        
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.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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Sake <tlep.nav.ekas at hccnet.nl> writes:

            

      
      
      
    

        
There are many tools in the R / Bioconductor project that address
these types of issues; a typical use case might use one of the 'org'
packages, e.g., org.Hs.eg.db though there are many others, to extract
information or to map between inforamtion types.

            

      
      
      
    

        
[snip]

            

      
      
      
    

        
gene_id start_location Chromosome
1    1000      -23784933         18
2   10000     -241718157          1
3   10000     -241733106          1

            

      
      
      
    

        
gene_id symbol
1    1000   CDH2
2   10000   AKT3

There are a number of packages for displaying this information, but
usually in conjunction with additional covariates.  GenomeGraphs
provides really pretty pictures (though is more for detailed
presentation of individual genes). rtracklayer is an interface that
lets you lay and navigate tracks on web-based genome browsers.

The place to start with Bioconductor is http://bioconductor.org, e.g.,

  basic install: http://bioconductor.org/docs/install/
  package list: http://bioconductor.org/packages/release/Software.html

            

      
      
      
    

        
Look to the AnnotationDbi 'vignettes', either on-line (link to the
AnnotationDbi package page from the list above) or in the package
itself (via openVignettes()).

Any follow-up questions about Bioconductor should go to the
Bioconductor mailing list

  http://bioconductor.org/docs/mailList.html

Martin