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

[Martin Morgan]

Sake  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', '1')])
  gene_id start_location Chromosome
11000  -23784933 18
2   1 -241718157  1
3   1 -241733106  1
> toTable(org.Hs.egSYMBOL[c('1000', '1')])
  gene_id symbol
11000   CDH2
2   1   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
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

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Re: [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.
-- 
View this message in context: 
http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21497719.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

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

[Neil Shephard]

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


-- 
View this message in context: 
http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21497479.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.

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

[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 escribió:

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*

Bioteknología Saila / /Dpto Biotecnología/

NEIKER-Tecnalia

Apdo 46

01080 Vitoria-Gasteiz (SPAIN)

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

pgoikoet...@neiker.net 

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and provide commented, minimal, self-contained, reproducible code.

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

[Pablo G Goicoechea]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] How to create a chromosome location map by locus ID

[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
-- 
View this message in context: 
http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21474206.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.