---------- Forwarded message ---------- From: Michael Lawrence <michafla@gene.com> Date: Thu, Feb 2, 2012 at 4:14 PM Subject: Re: [BioC] findOverlaps with strand info To: "Cook, Malcolm" <mec@stowers.org> Cc: Michael Lawrence <lawrence.michael@gene.com> On Thu, Feb 2, 2012 at 4:11 PM, Cook, Malcolm <mec@stowers.org> wrote: > > > On 2/2/12 5:57 PM, "Michael Lawrence" <lawrence.michael@gene.com> wrote: > > >On Thu, Feb 2, 2012 at 2:12 PM, Chris Stubben <stubben@lanl.gov> wrote: > > > >> Does anyone know how to add strands and number of overlapping bases to > >>the > >> findOverlaps output? For example, given these locations > >> > >> x <- GRanges( "chr", > >> IRanges( c(3,11,17,25,28), c(9,18,24,31,35)) , > >> c("-", "+", "+","-","+" )) > >> > >> and the findOverlaps output... > >> > >> y<- as.matrix(findOverlaps(ranges(**x), ignoreSelf=TRUE, > >> ignoreRedundant=TRUE)) > >> y > >> query subject > >> [1,] 2 3 > >> [2,] 4 5 > >> > >> I'd like to add the query and subject strands and number of overlapping > >> bases > >> > >> query subject strands overlap > >> 2 3 ++ 2 > >> 4 5 -+ 4 > >> > >> > >The query and subject columns index into the original ranges, so just > >index > >into their strand() to get the strands, i.e., strand(x)[y[,"query"]. You > >can then paste() that together. To get the amount of overlap, use > >width(pintersect(x[y[,"query"]], x[y[,"subject"]])). > > pintersect will complain about strand incompatibility, so I think this is > not quite right.... > > Sorry, just use ranges(x) there instead of 'x'. > > > > >I'm assuming you know how to combine the match matrix with other fields > >into a data.frame. > > > >Btw, in devel we have made RangesMatching contain Vector so it supports > >element metadata. This would be a good use case. > > > >Michael > > > > > >> Thanks, > >> Chris Stubben > >> > >> > >> > >> -- > >> Los Alamos National Lab > >> BioScience Division > >> MS M888 > >> Los Alamos, NM 87545 > >> > >> ______________________________**_________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> > >>https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.ch > >>/mailman/listinfo/bioconductor> > >> Search the archives: http://news.gmane.org/gmane.** > >> > >>science.biology.informatics.**conductor< > http://news.gmane.org/gmane.scien > >>ce.biology.informatics.conductor> > >> > > > > [[alternative HTML version deleted]] > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@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]]