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Question: ChIPpeakAnno
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6.2 years ago by
Bogdan520
Palo Alto, CA, USA
Bogdan520 wrote:
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 [[alternative HTML version deleted]]
modified 11 months ago by jun.yu0 • written 6.2 years ago by Bogdan520
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6.2 years ago by
Bogdan520
Palo Alto, CA, USA
Bogdan520 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]]
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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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11 months ago by
jun.yu0
jun.yu0 wrote:

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.

Here is an example:

https://bioconductor.org/packages/devel/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.html#section410