[BioC] ChIPpeakAnno question--peak aggregation over bins from TSS

[Kamesh Narasimhan]

Hi Julie,

Thanks a lot for your reply. Yes, it would indeed be very valuable to have such a an aggregate function in bioconductor. I would vote for that.

Thanks a lot
kamesh

-----Original Message-----
From: Zhu, Lihua (Julie) [mailto:Julie.Zhu at umassmed.edu] 
Sent: Thursday, January 17, 2013 11:09 AM
To: Kamesh Narasimhan; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS

Kamesh,

Thanks for sharing the interesting idea! Currently ChIPpeakAnno does not have function to do that. If there is a need, we are happy to add such functionality.

Best regards,

Julie


On 1/16/13 8:49 PM, "kamesh" <kamesh.narasimhan at utoronto.ca> wrote:

> Hi ,
> 
> I am new to using ChIPpeakAnno and find it to be a very useful tool 
> for ChIP-seq data processing. One question I have is, given an 
> annotated data of TSS sites, would it be possible using ChIPpeakAnno 
> to aggregate and obtain mean/median of signals (for eg: ChIP-TF 
> signal)in bins around the TSS comparable to the ACT tool referenced 
> here (http://info.gersteinlab.org/ACT_IntegratedExample).
> 
> Thanks
> 
> kamesh
> university of Toronto
> 
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