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@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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: output.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20130117="" 285d6f71="" attachment.txt="">

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@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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >