[BioC] ChIPpeakAnno on pathway enrichment

[Yuan Hao]

Dear Julie,

Thanks a million for the prompt response! It's really efficient! I am  
recently hooked by some other types of data, and will give it a go  
when I get a chance. I believe it will benefit many others at the same  
time. Thanks again for both you and Jianhong!

Cheers,
Yuan

On 15 Mar 2012, at 14:09, Zhu, Lihua (Julie) wrote:

> Dear Yuan,
>
> Per your request, Jianhong has added the function getEnrichedPATH in
> ChIPpeakAnno 2.3.3 (revision 63952 in dev repository).  Please type
> help(getEnrichedPATH) for examples.  Please let us know how it works  
> out for
> you.
>
> Thanks for the great suggestions!
>
> Best regards,
>
> Julie
>
>
> On 3/12/12 1:58 PM, "Yuan Hao" <yuan.x.hao at gmail.com> wrote:
>
>> Hi Julie,
>>
>> I used to do GSEA and Hypergeometric test on GO or KEGG (R/
>> Bioconductor "GOstats" , "GSEAlm" packages). KEGG seems the most
>> common database for pathways, but there are a couple of others (such
>> as those included in MsigDB) available. In terms of hypergeometric
>> test, the ideas behind either GO or KEGG are exactly the same. In the
>> later case, a single pathway is equivalent to a GO term. KEGG is a
>> collection of pathways and peaks from a ChIP-Seq experiment would
>> serve as selected genes. I attached a file contains pathways from
>> three databases retrieved from MsigDB, i.e. KEGG, BIOCARTA and
>> REACTOME. Thanks again for your reply!
>>
>> Regards,
>> Yuan
>>
>>
>>
>>
>> On 12 Mar 2012, at 00:38, Zhu, Lihua (Julie) wrote:
>>
>>> Dear Yuan,
>>>
>>> Thank you very much for your kind words! What kind of pathway are  
>>> you
>>> looking for? If you could share your thoughts on the type of pathway
>>> analysis and give us a couple of examples or tools, we will see if
>>> we could
>>> add that to the package.
>>>
>>> Many thanks for sharing the great ideas!
>>>
>>> Best regards,
>>>
>>> Julie
>>>
>>>
>>> On 3/11/12 3:56 PM, "Yuan Hao" <yuan.x.hao at gmail.com> wrote:
>>>
>>>> Hi Julie,
>>>>
>>>> ChIPpeakAnno is a really powerful and user friendly package. Thanks
>>>> first for the great job! The package implemented hypergeometric  
>>>> test
>>>> on GO enrichment analysis. I am wondering would it be possible to
>>>> include the similar function on pathways?
>>>>
>>>> Regards,
>>>> Yuan
>>>
>>>
>>
>>
>
>