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

[Zhu, Lihua (Julie)]

Thanks, Kamesh!

Best regards,

Julie


On 1/17/13 4:04 PM, "Kamesh Narasimhan" <kamesh.narasimhan at utoronto.ca>
wrote:

> 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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>> 
>