I think that Dario was in fact aiming for a single range that spanned the
entire alignment, including the gap between the ends, so a granges() method
would make sense here. Looks like you're most of the way towards
implementing it ;)

Michael



On Wed, Mar 20, 2013 at 10:05 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote:

> Hello,
>
> There are a couple of existing methods of GappedAlignmentPairs that may be
> helpful.
>
> Using 'galp' from the man page as an example,
>
> example(GappedAlignmentPairs)
> > class(galp)
> [1] "GappedAlignmentPairs"
> attr(,"package")
> [1] "GenomicRanges"
> > length(galp)
> [1] 1572
>
> To get your furthest outer positions, pull out the start of the left-most
> pair and the end of the right-most pair:
>
> outer <- cbind(start(left(galp)), end(right(galp)))
> > head(outer)
>      [,1] [,2]
> [1,]   36  219
> [2,]   49  259
> [3,]   51  262
> [4,]   60  259
> [5,]   60  269
> [6,]   61  282
>
> For coverage, the left and right pair can be extracted and coerced to a
> GRAnges which retains introns in each pair as part of the range.
>
> grleft <- granges(left(galp))
> grright <- granges(right(galp))
>
> If we implemented a granges,GappedAlignmentPairs it should return
> something of the same length. To do this we'd have to merge the pair ranges
> which would then include the space between the ranges which I don't think
> we want. Right?
>
> As an fyi, another potentially useful function is introns(). This returns
> a GRangesList of all intron ranges for each pair.
>
> introns <- introns(galp)
>
>
> Valerie
>
>
> On 03/19/2013 09:44 PM, Michael Lawrence wrote:
>
>> It would make sense for this to be granges,GappedAlignmentPairs. Want to
>> contribute it?
>>
>> Michael
>>
>>
>> On Tue, Mar 19, 2013 at 5:59 PM, Dario Strbenac <d.strbenac@garvan.org.au
>> >**wrote:
>>
>>  Hello,
>>>
>>> I would like to calculate the furthest outer positions of the mapped read
>>> pairs. That is, the lowest and highest mapped coordinate of a read. In a
>>> later step, I want to get a coverage estimate that also includes coverage
>>> of the spliced out intron parts. I couldn't find any function already in
>>> GenomicRanges. I made my own code to create a GRanges object of these
>>> simple ranges, but was curious about any API functionality I overlooked
>>> that could do this.
>>>
>>> Thanks,
>>>             Dario.
>>>
>>> ------------------------------**--------
>>> Dario Strbenac
>>> PhD Student
>>> University of Sydney
>>> Camperdown NSW 2050
>>> Australia
>>> ______________________________**_________________
>>> Bioconductor mailing list
>>> Bioconductor@r-project.org
>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>>> Search the archives:
>>> http://news.gmane.org/gmane.**science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>>
>>>
>>         [[alternative HTML version deleted]]
>>
>>
>> ______________________________**_________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> Search the archives: http://news.gmane.org/gmane.**
>> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>>

	[[alternative HTML version deleted]]

