Hi, I have some R-scripts that rely on the argument multiple=TRUE in findOverlaps(). However, this option has been removed in the latest release it seems, as it was said to be deprecated before. But now our scripts don't work any more, and removing the parameter simply yields a different output format and is not an option. Is there a quick way to bring the behavior of it back, with respect to output format and overlap matching? Thank you very much for your help Michael

Hi Michael, On Sat, Apr 28, 2012 at 3:23 AM, <michael.dondrup at="" uni.no=""> wrote: > Hi, > I have some R-scripts that rely on the argument multiple=TRUE > in findOverlaps(). However, this option has been removed in the latest > release it seems, as it was said to be deprecated before. But now > our scripts don't work any more, and removing the parameter > simply yields a different output format and is not an option. > > Is there a quick way to ?bring the behavior of it back, with respect to > output format and overlap matching? I'm sure the folks at bioc-central will recall exactly how multiple=TRUE does, but some of us have a harder time remembering the ins/outs of the findOverlaps internals but would still like to try to help ;-) Could you maybe provide a small example (few ranges in the query, a few in the subject) that would result in a findOverlaps() call w/ multiple overlaps and show us what you'd like to get out of it so that your scripts can keep humming? Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

I think you just want to use the "select" argument. For example, multiple=FALSE before would correspond to select="arbitrary" now, while multiple=TRUE corresponds to the default select="all". There are other values for select. Michael On Sat, Apr 28, 2012 at 12:23 AM, <michael.dondrup@uni.no> wrote: > Hi, > I have some R-scripts that rely on the argument multiple=TRUE > in findOverlaps(). However, this option has been removed in the latest > release it seems, as it was said to be deprecated before. But now > our scripts don't work any more, and removing the parameter > simply yields a different output format and is not an option. > > Is there a quick way to bring the behavior of it back, with respect to > output format and overlap matching? > > Thank you very much for your help > Michael > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]