Hi Kasper, This is fixed in GenomicRanges 1.3.15 (devel). Cheers, H. On 01/13/2011 11:17 PM, Hervé Pagès wrote: > Hi Kasper, > > Thanks for the report. I'll take care of this and will come back > here when it's done. > > H. > > On 01/13/2011 09:09 AM, Kasper Daniel Hansen wrote: >> GenomicRanges::findOverlaps does not support the same set of values >> for 'select' and 'type' as the method for Ranges. This is pretty easy >> to fix, and seems to arise because the GenomicRanges version has the >> usual >> function( ... type = c(...)) { >> type = match.arg(type) >> } >> construction, but with type = c("any", "start", "end") instead of type >> = c("any", "start", "end", "within", "equal"). A better long term fix >> might be to not do the match.arg inside the method, but directly pass >> the value of type and select into .findOverlaps.circle (which btw. >> does exactly this: it simply passes the type and select arguments into >> findOverlaps) >> >> I am specifically interested in type = "within" >> >> Kasper >> >> _______________________________________________ >> 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 > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319