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 Thanks, Chris Stubben -- Los Alamos National Lab BioScience Division MS M888 Los Alamos, NM 87545

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"]])). 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.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]]