Hi Bioconductor folks, I'm trying to create some GRanges summaries, but I think I may be missing an obvious solution. I have fixed-width windows as a GRanges object, and for each window/row I'd like to add a metadata column that indicates how many base pairs of this window overlap features in another GRange object. I'll need to add a few columns for different features in different GRanges objects. I've tried using the approach of findOverlaps, followed by ranges() to extract range widths. This creates an error: "'query' must be a Ranges of length equal to number of queries". I saw in the source that pintersect(query[queryHits(x)], subject[subjectHits(x)]) works too (and does without error). This returns the overlapping ranges, but it'd take a load of data munging to get it into the format I'd like — it seems like I may be overlooking an easier solution. thanks, Vince !> sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin13.0.1 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] ggplot2_0.9.3.1 rtracklayer_1.22.0 GenomicRanges_1.14.3 [4] XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0 [7] ESSR_1.0.1 loaded via a namespace (and not attached): [1] Biostrings_2.30.1 bitops_1.0-6 BSgenome_1.30.0 colorspace_1.2-4 [5] compiler_3.0.2 dichromat_2.0-0 digest_0.6.4 grid_3.0.2 [9] gtable_0.1.2 labeling_0.2 MASS_7.3-29 munsell_0.4.2 [13] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 [17] reshape2_1.2.2 Rsamtools_1.14.2 scales_0.2.3 stats4_3.0.2 [21] stringr_0.6.2 tools_3.0.2 XML_3.98-1.1 zlibbioc_1.8.0 -- Vince Buffalo Ross-Ibarra Lab www.rilab.org) Plant Sciences, UC Davis [[alternative HTML version deleted]]