Supposing I wanted to do this with several hundred tumors to look for
hotspots in certain subtypes, is there a convenient way to do this
internally with one or two great big GRanges?  Or is this the sort of
situation where I should use a genoset?

Example (CNV.GR is a GRanges for a tumor type, built from GISTIC CNV calls
achieving regional statistical significance):

> EZH2 <- getCNV('EZH2', CNV.GR) # subsetByOverlaps(CNV.GR, getExons(gene,
basesUp))
> head(EZH2)
GRanges with 6 ranges and 1 elementMetadata value:
               seqnames                 ranges strand |     score
                  <Rle>              <IRanges>  <Rle> | <numeric>
  2915.Del.170     chr7 [140579242, 159118025]      * |        -1
   2952.Del.93     chr7 [141787637, 157040032]      * |        -1
  2929.Del.258     chr7 [141956277, 148251831]      * |        -1
   2874.Del.44     chr7 [142484285, 159127005]      * |        -1
   2857.Del.97     chr7 [142486080, 154885611]      * |        -1
   2805.Del.78     chr7 [142486080, 154970916]      * |        -1
> sum(score(EZH2))
[1] -22

So exons of EZH2 are frequently deleted in the particular set of samples
I'm looking at.  Myc is amplified a great deal.  etc. But I knew what I
wanted to look for in those cases.  Suppose I instead want to blob together
and scan various tumors by common mutations, or known subtypes of driver
mutations.  It's handy for me to just slap a +1 or -1 in the 'score' column
and add it up.  It would be handier still for me to do running tallies of
this... it seems like the sort of thing that people would have solved years
ago, I just don't know precisely what to look for in terms of documentation
for it.

Any assistance is appreciated.

--t



On Tue, Dec 13, 2011 at 8:55 AM, Daniel Brewer <Daniel.Brewer@icr.ac.uk>wrote:

> Thanks Martin,
>
> Yes you're right a simple intersect works great.  I had a suspicion I was
> missing something very obvious.  Many thanks.
>
> Dan
>
> On 13 Dec 2011, at 4:49 PM, Martin Morgan wrote:
>
> > On 12/13/2011 07:00 AM, Daniel Brewer wrote:
> >> Dear mailing list,
> >>
> >> I have two GRanges objects each containing segments of copy number
> >> change for a tumour.  I would like to find regions where there is
> >> copy number change in both the tumours.  I though findOverlaps was
> >> giving me what I wanted but soon found that findOverlaps(A,B) !=
> >> findOverlaps(B,A).  I am sure there must be a reasonable way to do
> >> this but I cannot find it.
> >
> > Hi Dan --
> >
> >> a = GRanges("chrA", IRanges(11, 20), seqlengths=c(chrA=100))
> >> b = GRanges("chrA", IRanges(16, 25), seqlengths=c(chrA=100))
> >> intersect(a, b)
> > GRanges with 1 range and 0 elementMetadata values:
> >       seqnames    ranges strand
> >          <Rle> <IRanges>  <Rle>
> >   [1]     chrA  [16, 20]      *
> >   ---
> >   seqlengths:
> >    chrA
> >     100
> >
> > but maybe a working example from your end would help clarify what you're
> > after / where things go wrong for you with findOverlaps.
> >
> > Martin
> >
> >>
> >> Thanks
> >>
> >> Dan
> >>
> >
> >
> > --
> > Computational Biology
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >
> > Location: M1-B861
> > Telephone: 206 667-2793
>
> --
> **************************************************************
>
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
> Molecular Carcinogenesis
> MUCRC
> 15 Cotswold Road
> Sutton, Surrey SM2 5NG
> United Kingdom
>
> Tel: +44 (0) 20 8722 4109
>
> **************************************************************
>
>
>
>
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