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

[Martin Morgan]

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

> 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.

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.

> library(org.Hs.eg.db)
> ls(2)
[snip]
> toTable(org.Hs.egCHRLOC[c('1000', '10000')])
  gene_id start_location Chromosome
1    1000      -23784933         18
2   10000     -241718157          1
3   10000     -241733106          1
> toTable(org.Hs.egSYMBOL[c('1000', '10000')])
  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

> source('http://bioconductor.org/biocLite.R')
> biocLite() # default packages
> biocLite('org.Hs.eg.db') #  specific package
> library(org.Hs.eg.db)

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


> 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.
> -- 
> View this message in context: http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21497719.html
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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