Hi, thank you both - very helpful. Janet On Mar 27, 2012, at 6:35 AM, Valerie Obenchain wrote: > Hi Janet, Malcom, > > Yes, we can add distanceToNearest for GRanges. This will probably happen after the release (i.e., next week). I'll post back here when it's complete. > > Valerie > > > On 03/26/12 16:26, Cook, Malcolm wrote: >> Janet, >> >> In the mean time.... >> >> distanceToNearest.GRanges<- function (query,subject=query,...,.AS=DataFrame) { >> ## PURPOSE: an implementation of distanceToNearest for GRanges in >> ## terms of 'nearest' and 'distance' whose return value is shaped >> ## like that of IRange's 'nearest', by default, but you can ask for >> ## the result .AS=data.table or .AS=data.frame if you prefer. >> if(missing(subject)) { >> nearestSubjectIndex<-nearest(query,...) >> } else { >> nearestSubjectIndex<-nearest(query,subject,...) >> } >> queryHasNearest<-! is.na(nearestSubjectIndex) >> queryIndex<-which(queryHasNearest) >> queryHavingNearest<-query[queryIndex] >> nearestSubjectIndex<-nearestSubjectIndex[queryIndex] >> nearestSubject<-subject[nearestSubjectIndex] >> d<-distance(queryHavingNearest,nearestSubject) >> .AS(query=queryIndex >> ,subject=nearestSubjectIndex >> ,distance=d) >> } >> >> You've asked so many questions in this forum whose answer I made use of that I must owe you this tidbit.... >> >> Lurkers, and fellow travelers, I welcome corrections and stylistic suggestions. >> >> Cheers, >> >> Malcolm Cook >> >> >> ________________________________________ >> From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Janet Young [jayoung at fhcrc.org] >> Sent: Monday, March 26, 2012 4:42 PM >> To: bioconductor at r-project.org >> Subject: [BioC] distanceToNearest for GRanges? >> >> Hi there, >> >> Any plans to implement distanceToNearest for GRanges objects? That would be really useful for me. >> >> thanks, >> >> Janet >> >> >> ------------------------------------------------------------------- >> >> Dr. Janet Young >> >> Tapscott and Malik labs >> >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Avenue N., C3-168, >> P.O. Box 19024, Seattle, WA 98109-1024, USA. >> >> tel: (206) 667 1471 fax: (206) 667 6524 >> email: jayoung ...at... fhcrc.org >> >> >> ------------------------------------------------------------------- >> >> _______________________________________________ >> 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 >