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

[Kamesh Narasimhan]

Hi Julie,

Just to add on to my previous mail. Further optional controls could be like.

1. Radius-- number of base pairs from a feature site like TSS

2. nbins--- specify how many bins in the flanking region of a feature site like TSS.

Thanks once again for your interest in developing this functionality in ChIPpeakAnno.

Best 
kamesh


-----Original Message-----
From: Kamesh Narasimhan 
Sent: Thursday, January 17, 2013 3:44 PM
To: 'Zhu, Lihua (Julie)'; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS

Hi Julie,

Thanks a lot for your reply. I am attaching the input files factor1.bed (TF signal file), hg17_ensembl.bed(annotation file), and the aggregated output (median of each bin). It would in principle to have options to plot mean/median/stdev of signals in each bin. 

An example of such a functionality is here http://tiling.mbb.yale.edu/frame1.html with example input/output files.

Best
kamesh

-----Original Message-----
From: Zhu, Lihua (Julie) [mailto:Julie.Zhu at umassmed.edu] 
Sent: Thursday, January 17, 2013 3:29 PM
To: Kamesh Narasimhan; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] ChIPpeakAnno question--peak aggregation over bins from TSS

Kamesh,

Would you be interested in sending me a small test input and expected output for the new functionality? Thanks!

Best regards,

Julie


On 1/17/13 11:30 AM, "Kamesh Narasimhan" <kamesh.narasimhan at utoronto.ca>
wrote:

> 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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>