[BioC] ChIPPeakAnno query (overlaps)

[Zhu, Lihua (Julie)]

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/ChIPpeakAnno/
>> 
>> 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
>>>>>> 
>>>>> 
>>>> 
>>> 
>>> 
>> 
> 
>