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

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