Dear list, I have a GRanges object that contains some ranges that are completely contained within larger ranges as well as ranges that overlap. I know I can use reduce to merge overlapping ranges and remove the smaller, completely contained, ranges. However, I would like to only remove ranges that are completely within a larger range and leave overlapping ranges intact. For example, > g <- GRanges(seqnames = Rle('chr1', 3), ranges = IRanges(start = c(1, 3, 8), end = c(10, 7, 15))) > reduce(g) GRanges with 1 range and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> [1] chr1 [1, 15] * --- seqlengths: chr1 NA I would like to to get the following GRanges: GRanges with 1 range and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> [1] chr1 [1, 10] * [2] chr1 [8, 15] * --- seqlengths: chr1 NA Does anyone know if there's an easy way to do this with GRanges? Thanks, Jonathan

Like this: g[is.na(findOverlaps(g, type="within", ignoreSelf=TRUE, select="arbitrary"))] With devel IRanges, this is also possible: g[!overlapsAny(g, type="within", ignoreSelf=TRUE)] Michael On Fri, Jun 6, 2014 at 12:18 AM, Jonathan Ellis < Jonathan.Ellis@qimrberghofer.edu.au> wrote: > Dear list, > > I have a GRanges object that contains some ranges that are completely > contained within larger ranges as well as ranges that overlap. I know I > can use reduce to merge overlapping ranges and remove the smaller, > completely contained, ranges. However, I would like to only remove > ranges that are completely within a larger range and leave overlapping > ranges intact. For example, > > > g <- GRanges(seqnames = Rle('chr1', 3), > ranges = IRanges(start = c(1, 3, 8), end = c(10, 7, 15))) > > reduce(g) > GRanges with 1 range and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > [1] chr1 [1, 15] * > --- > seqlengths: > chr1 > NA > > I would like to to get the following GRanges: > > GRanges with 1 range and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > [1] chr1 [1, 10] * > [2] chr1 [8, 15] * > --- > seqlengths: > chr1 > NA > > Does anyone know if there's an easy way to do this with GRanges? > > Thanks, > Jonathan > > _______________________________________________ > 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]]