Thanks all for your reply. Just tried ChIPpeakAnno, it is doing well. Cheers. -----Original Message----- From: Tim Triche, Jr. [mailto:tim.triche@gmail.com] Sent: Tuesday, July 10, 2012 6:47 PM To: Jonathan Cairns Cc: Nicolas DESCOSTES; bioconductor at r-project.org Subject: Re: [BioC] IRanges problem: findOverlaps how about resize(genes,1, fix='start') findOverlaps(peaks, genes) however, +1 for Julie Zhu's ChIPpeakAnno package since, as was just pointed out, it is meant for such things! On Tue, Jul 10, 2012 at 9:43 AM, Jonathan Cairns <jonathan.cairns at="" cancer.org.uk=""> wrote: > Hi, > > >From ?findOverlaps: > > "If 'type' is 'start' or 'end', the intervals are required to have matching starts or ends, respectively." > > This doesn't sound like it's what you're after, as type = "start" considers only the starts of peaks, as well as the starts of whatever annotation you're using. > > Have you looked at the package ChIPpeakAnno? It is designed for annotating ChIP-seq peaks and might be useful. > > Jonathan > > ________________________________________ > From: bioconductor-bounces at r-project.org > [bioconductor-bounces at r-project.org] On Behalf Of Nicolas DESCOSTES > [descostes at ciml.univ-mrs.fr] > Sent: 10 July 2012 16:40 > To: bioconductor at r-project.org > Subject: [BioC] IRanges problem: findOverlaps > > Dear members, > > I have a set of chip-Seq peaks which I want to find the overlap with a bench of annotations downloaded from ucsc. > > When I am doing the overlap between my peaks and annotations list, I am finding 5635 positive matches. When adding "type = "start"", I have no results returned. However, when I am visualizing the 5635 intervals, it overlaps many start site of my genes annotations. > > I tried to update IRanges but I am still getting no results. > > Any idea? > > Thanks. > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > NOTICE AND DISCLAIMER > This e-mail (including any attachments) is intended for > ...{{dropped:16}} > > _______________________________________________ > 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 -- A model is a lie that helps you see the truth. Howard Skipper

Hi all, I'm not sure about intervals, but genomeIntervals is chromosome-aware (http://bioconductor.org/packages/release/bioc/html/genomeIntervals.ht ml). The syntax is as described by Alex, since genomeIntervals extends intervals. Whether you use genomeIntervals or IRanges is just a matter of taste, really. Cheer, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Jul 10, 2012, at 6:34 PM, Ivan Gregoretti wrote: > Hi Alex, > > I am not sure interval_overlap() is better option than findOverlaps(). > > Is interval_overlap() aware that intervals may lie in different chromosomes? > > In other words, every peak has three coordinates: chromosome, start > and end. The findOverlaps() function is aware of that. > > Thank you, > > Ivan > > > Ivan Gregoretti, PhD > > > On Tue, Jul 10, 2012 at 12:05 PM, alessandro brozzi > <alessandro.brozzi at="" gmail.com=""> wrote: >> hi Nicolas, >> >> I don't know very well Iranges but to find overlapping intervals the >> package "intervals" >> >> http://cran.fhcrc.org/web/packages/intervals/index.html >> >> is very straightforward. >> >> Here an example: >> >> peaks = matrix( >> c( >> 2, 8, >> 8, 9, >> 6, 9, >> 11, 12, >> 3, 3 >> ), >> ncol = 2, byrow = TRUE >> ) >> >>> peaks >> [,1] [,2] >> [1,] 2 8 >> [2,] 8 9 >> [3,] 6 9 >> [4,] 11 12 >> [5,] 3 3 >>> >> >> track = matrix( >> c( >> 2, 8, >> 3, 4, >> 5, 10 >> ), >> ncol = 2, byrow = TRUE >> ) >> >> track >> [,1] [,2] >> [1,] 2 8 >> [2,] 3 4 >> [3,] 5 10 >> >> interval_overlap ( Intervals(peaks), Intervals(track)) >> >> [[1]] >> [1] 1 2 3 >> >> [[2]] >> [1] 1 3 >> >> [[3]] >> [1] 1 3 >> >> [[4]] >> integer(0) >> >> [[5]] >> [1] 1 2 >> >> the result is a list: for each peak you have the indexes of the >> corresponding overlapping items of the track matrix. Setting some options >> you can fine tune your research. >> >> HTH, >> Alex >> >> >> On Tue, Jul 10, 2012 at 5:40 PM, Nicolas DESCOSTES < >> descostes at ciml.univ-mrs.fr> wrote: >> >>> Dear members, >>> >>> I have a set of chip-Seq peaks which I want to find the overlap with a >>> bench of annotations downloaded from ucsc. >>> >>> When I am doing the overlap between my peaks and annotations list, I am >>> finding 5635 positive matches. When adding "type = "start"", I have no >>> results returned. However, when I am visualizing the 5635 intervals, it >>> overlaps many start site of my genes annotations. >>> >>> I tried to update IRanges but I am still getting no results. >>> >>> Any idea? >>> >>> Thanks. >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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