[Bioc-sig-seq] Overlap of multiple RangedData instances.

[Ivan Gregoretti]

Hi Michael,

I think that I expressed myself too ambiguously.

I am looking for the multiple intersection. That is, I am looking for
the ranges in A that are even minimally overlapped by ranges in ALL
the rest of the RangesData instances. A super-dee-duper intersection.

The union() operation would be finding overlaps with ANY of the rest
of the RangesData.

At the moment, like Karl, I am evading the problem by dint of shameful
for loops.

Do you think that there is a more elegant way?

Thanks

Ivan


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878



On Tue, Mar 16, 2010 at 4:26 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
>
>
> On Tue, Mar 16, 2010 at 12:34 PM, Ivan Gregoretti <ivangreg at gmail.com>
> wrote:
>>
>> Hello everybody,
>>
>> Say A, B, C, D, .... are all RangedData instances.
>>
>> How do you come up with the list of ranges in A that have at least
>> some overlap with B, C, D, ...?
>>
>> I want to calculate the multiple intersection ignoring the extent of
>> the overlap.
>>
>> ?findOverlaps does not hint how to recover the ranges from A.
>>
>
> Something like:
> ranges(A) %in% union(union(ranges(B), ranges(C)), ranges(D))
>
> That syntax is a little verbose. I propose adding some operators to Ranges,
> RangesList and RangedData objects.
>
> "+" for union()
> "-" for setdiff()
> "!" for gaps()
>
> Then we could have:
> A %in% (B + C + D)
>
> What do people think?
>
>
>>
>> Thank you,
>>
>> Ivan
>>
>>
>> Ivan Gregoretti, PhD
>> National Institute of Diabetes and Digestive and Kidney Diseases
>> National Institutes of Health
>> 5 Memorial Dr, Building 5, Room 205.
>> Bethesda, MD 20892. USA.
>> Phone: 1-301-496-1592
>> Fax: 1-301-496-9878
>>
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>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>