Dear Sukhdeep, Thanks for the nice feedback and great suggestion! I have added minoverlap with default 1 bp to both findOverlappingPeaks and makeVennDiagram for the dev version with revision 65860. For a diagram generated from two datasets A and B, there are 4 numbers, i.e., nA: number of peaks unique to A, nB: number of peaks unique to B, nAB: number of peaks shared in A and B, totalTest – nA – nB – nAB. Best regards, Julie On 5/11/12 8:06 PM, "Sukhdeep Singh" <sukhdeepsingh.bio@gmail.com> wrote: Hello Dr.Zhu. I tried using ChIPPeakAnno, its really nice, just I am stuck in small thing. When I used findOverlappingPeaks or makeVennDiagram direclty, is there any parameter for specifying the minimum overlap between the peaks of two chip-seq profiles as being implement in the intersectBed of the Bedtools (-f paramter - 0.5 specifies 50-100% overlap is an overlap)and supposedly opposite to the maxgap. Logically, maxgap should also be able to take a -ve values so as to define the same thing, but may there's a custom code or already implemented technique. Also, when I make Venn Diagrams using the function I wrote above, what is the -ve number (0 by 0 case of 2 datasets) in the venn diagram on the right bottom. Thanks a lot, Sukhdeep Singh Dresden [[alternative HTML version deleted]]

Sukhi, Here is the access information. Thanks! user name: readonly password: readonly http://www.bioconductor.org/developers/source-control/ Best regards, Julie On 5/17/12 12:32 PM, "Sukhdeep Singh" <sukhdeepsingh.bio at="" gmail.com=""> wrote: > Thanks , but I need authorization to access it. Is it made protective!! > > Sukhi > > On 17 May 2012 18:26, Zhu, Lihua (Julie) <julie.zhu at="" umassmed.edu=""> wrote: >> Sukhdeep, >> >> You might want to get the most recent devel version 65988 at >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpea kAnno/ >> >> You could try to replace the relevant files in your ChIPpeakAnno/R >> directory. >> >> Best regards, >> >> Julie >> >> >> On 5/16/12 10:48 AM, "Sukhdeep Singh" <sukhdeepsingh.bio at="" gmail.com=""> wrote: >> >>> Thanks for taking it into account, When do you plan to release the package >>> with this update or can I get the devel version somewhere. >>> >>> Regards, >>> >>> Sukhdeep Singh >>> >>> On 14 May 2012 16:41, Sukhdeep Singh <sukhdeepsingh.bio at="" gmail.com=""> wrote: >>>> Great News, >>>> >>>> >>>> On May 14, 2012, at 4:28 PM, Zhu, Lihua (Julie) wrote: >>>> >>>>> Dear Sukhdeep, >>>>> >>>>> Thanks for the nice feedback and great suggestion! I have added minoverlap >>>>> with default 1 bp to both findOverlappingPeaks and makeVennDiagram for the >>>>> dev version with revision 65860. >>>>> >>>>> For a diagram generated from two datasets A and B, there are 4 numbers, >>>>> i.e., nA: number of peaks unique to A, nB: number of peaks unique to B, >>>>> nAB: >>>>> number of peaks shared in A and B, totalTest ? nA ? nB ? nAB. >>>>> >>>>> Best regards, >>>>> >>>>> Julie >>>>> >>>>> >>>>> On 5/11/12 8:06 PM, "Sukhdeep Singh" <sukhdeepsingh.bio at="" gmail.com=""> wrote: >>>>> >>>>>> Hello Dr.Zhu. >>>>>> I tried using ChIPPeakAnno, its really nice, just I am stuck in small >>>>>> thing. >>>>>> >>>>>> When I used findOverlappingPeaks or makeVennDiagram direclty, is there >>>>>> any >>>>>> parameter for specifying the minimum overlap between the peaks of two >>>>>> chip-seq profiles as being implement in the intersectBed of the Bedtools >>>>>> (-f paramter - 0.5 specifies 50-100% overlap is an overlap)and supposedly >>>>>> opposite to the maxgap. Logically, maxgap should also be able to take a >>>>>> -ve >>>>>> values so as to define the same thing, but may there's a custom code or >>>>>> already implemented technique. >>>>>> >>>>>> Also, when I make Venn Diagrams using the function I wrote above, what is >>>>>> the -ve number (0 by 0 case of 2 datasets) in the venn diagram on the >>>>>> right >>>>>> bottom. >>>>>> >>>>>> Thanks a lot, >>>>>> >>>>>> Sukhdeep Singh >>>>>> Dresden >>>>>> >>>>> >>>> >>> >>> >> > >