Hi Michael, thanks for the reply but I already tried to do setdiff and I get this message, Error in as.vector(x) : no method for coercing this S4 class to a vector My reads are not all of the same length, the read length varies from 18 to 26 bp, these are from a small RNA seq experiment. Thanks for the help. Kind regards, Andreia On Mon, Jul 4, 2011 at 12:24 AM, Michael Lawrence wrote: > > > On Sat, Jul 2, 2011 at 10:41 PM, Andreia Fonseca < > andreia.fonseca@gmail.com> wrote: > >> Dear all, >> >> I have a range list which I have created like this: >> >> aln<-readAligned("GHO-23_filtered.fastq_aligned", type="Bowtie") >> cvg = coverage(aln) >> islands <- slice(cov, lower = 1) >> ranges_islands <-slice(cvg, 1, rangesOnly=TRUE) >> >> And then I have a GRange object which I have imported >> >> genes=import.gff3("Egrandis_162_gene.gff3", asRangedData=FALSE) >> >> I want to select the ranges in ranges_islands which do not overlap with >> genes into object final_ranges and then I want to select the reads from >> aln >> which are within or overlapping >50% with object final_ranges. >> >> > If your reads are of a fixed length, then something like this should work: > > final_ranges <- setdiff(ranges_islands, genes) > final_aln <- aln[!is.na(findOverlaps(as(aln, "GRanges"), final_ranges, > select = "first", minoverlap = halfReadLength))] > > Michael > > > >> I also would like to export the object final_ranges to a table chr, start, >> end. >> >> Can someone help? >> Thanks >> Andreia >> >> >> ----------------------------------------------------------------------------------------------- >> Andreia J. Amaral, PhD >> BioFIG - Center for Biodiversity, Functional and Integrative Genomics >> Instituto de Medicina Molecular >> University of Lisbon >> Tel: +352 217500000 (ext. office: 28253) >> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt >> >> [[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 >> > > -- --------------------------------------------------------------------------------------------- Andreia J. Amaral, PhD BioFIG - Center for Biodiversity, Functional and Integrative Genomics Instituto de Medicina Molecular University of Lisbon Tel: +352 217500000 (ext. office: 28253) email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]