Dear all,
for people that have experience with ChIPpeakAnno:
please could you let me know in more detail the meaning of "totalTest
" in
"makeVennDiagram" function ;
as depending on the totalTest value, the p-value can change
significantly.
thanks a lot,
Bogdan
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Dear all,
regarding the ChIPpeakAnno package, particularly on the
"makeVennDiagram"
function, please could you let me know on how the significance p-value
of
the intersected peaks is computed. thanks a lot,
Bogdan
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Hi Bogdan,
The output p-vlaue of makeVennDiagram is obtained from hypergeometric
test.
You can try
> ?hyper
to get more info.
Yours sincerely,
Jianhong Ou
jianhong.ou at umassmed.edu
On Jul 10, 2012, at 2:40 PM, Bogdan Tanasa wrote:
> Dear all,
>
> regarding the ChIPpeakAnno package, particularly on the
"makeVennDiagram"
> function, please could you let me know on how the significance
p-value of
> the intersected peaks is computed. thanks a lot,
>
> Bogdan
>
> [[alternative HTML version deleted]]
>
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The p-value is calculated by hypergeometric test to determine whether the peaks or features are overlapped significantly in the makeVennDiagram function. Hypergeometric test requires users to input an estimate of the total potential binding sites (peaks) for a given TF. To circumvent this requirement, a permutation test function called permTest has also been implemented in ChIPpeakAnno package.
