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

[Dave Clements, GMOD Help Desk]

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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