Re: [Useq-users] IntersectRegions Output

[David N. <dav...@gm...>]

Hello Richard,

The pval is based not on the total bp but on the number of regions that
intersect.  The average is actually the average number of intersections
observed from the random trials.  This lets one calculate a fold
enrichment over the random for a given real intersection between your
region lists.  

Yes, the random intervals could be outputted to file.  If this is
something you would really really like then put in a feature request on
USeq Sourceforge.

-cheers, D

On 3/1/12 7:52 AM, "Baker, Richard" <Ric...@um...> wrote:

>I'm not sure I completely understand the output from IntersectRegions,
>but it looks as though the randomization P value is the fraction of
>trials in which the total bp intersected equals or exceeds the that of
>the actual query.  Is it possible to determine the average number of
>random intervals "hit" per trial (as opposed to total bp)?
>Alternatively, could the program be easily modified to output the random
>regions into a file?  This would be extremely useful, and I've not found
>another tool that does this.
>
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