Hi, I am investigating the interplay of different isoforms, in alternative splicing differential expression. I would like to compare coverage profiles of the same isoform with or without the presence of the other isoforms, there is any tool, in bioconductor, that allows manipulation of coverage profile, e.g. subtraction of a profile to an other or comparison between different coverage profiles? Cheers Raffaele -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0112366457 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it

Dear Raffaele since coverage is simply a vector along genomic coordinates, would perhaps the basic vector arithmetic from R's base package, or perhaps the Rle class from the IRanges package be applicable? Best wishes Wolfgang On 10 Sep 2013, at 08:36, rcaloger <raffaele.calogero at="" gmail.com=""> wrote: > Hi, > I am investigating the interplay of different isoforms, in alternative splicing differential expression. > I would like to compare coverage profiles of the same isoform with or without the presence of the other isoforms, there is any tool, in bioconductor, that allows manipulation of coverage profile, e.g. subtraction of a profile to an other or comparison between different coverage profiles? > Cheers > Raffaele > > -- > > ---------------------------------------- > Prof. Raffaele A. Calogero > Bioinformatics and Genomics Unit > MBC Centro di Biotecnologie Molecolari > Via Nizza 52, Torino 10126 > tel. ++39 0116706457 > Fax ++39 0112366457 > Mobile ++39 3333827080 > email: raffaele.calogero at unito.it > raffaele[dot]calogero[at]gmail[dot]com > www: http://www.bioinformatica.unito.it > > _______________________________________________ > 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