[Gmod-gbrowse] [Gmod-help] How to put info about "association analysis (p value)" in Gbrowse

[Yinyan Guo]

Dear Oliver,

Many thanks for your great help. Yes, It is the type of glyph that I am 
looking for. Please send me an example of conf.

Thank you again for your great help.

Sincerely

Yinyan




Oliver Burren <oliver.burren at cimr.cam.ac.uk> 
2010-01-28 11:55

To
"Dave Clements, GMOD Help Desk" <help at gmod.org>
cc
Yinyan Guo <Yinyan.Guo at dnalandmarks.ca>, 
gmod-gbrowse at lists.sourceforge.net
Subject
Re: [Gmod-gbrowse] [Gmod-help] How to put info about "association analysis 
(p value)" in Gbrowse






Dear Yinyan,

Is this something similar to what you are trying to achieve ?

http://tinyurl.com/yfzutqa

If so let me know and I'll be happy to help out by sending example conf 
file etc.

Thanks,

Olly Burren

Dave Clements, GMOD Help Desk wrote:
> Dear Yinyan,
> 
> I've cc'd the GBrowse list, which is the best place to post these 
discussions.
> 
> On Mon, Jan 25, 2010 at 2:07 PM, Yinyan Guo <Yinyan.Guo at dnalandmarks.ca> 
wrote:
>> Dear Sir,
>>
>> Gbrowse is very good tool to browse genome info (SNP, gene, etc).  Its 
data
>> structure is simple.
>>
>> In association analysis, I have p value for each marker, Is there any 
method
>> to put those p value (line) in Bbrowse?
> 
> I can think of a couple of ways to do this, depending on your
> situation.  If you aren't already using colors (or height or ...) for
> something else, you could set the color of the marker based on its p
> value.  This would be done by putting the p value in column 9 of the
> GFF and using it in a small perl callout routine.  You could also have
> a separate p-value track where you just show p values, again using
> something like color or height.  You can also show p-values in popups
> or link out pages, but then the user has to take some additional
> action to see the information.
> 
> I'm not too familiar with association studies.  Are the p values
> associated with alleles/variants, or is there at most one p-value per
> region?  If there is only one p-value per region, or if you are at low
> zoom (zoomed out), you could show the p-values with an xyplot.
> 
> Does that help?
> 
> Dave C.
>> Thank you in advance for your support.
>>
>> Sincerely
>>
>> Yinyan
>>
> 
> 
> 


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