I see. So I assume the p in pmap stands for paired?.
Any ballpark as to when this implementation will be added?


On Fri, Mar 21, 2014 at 3:59 PM, Michael Lawrence <lawrence.michael@gene.com
> wrote:

> Yea, pmap() would do ranges[x] to grangeslist[x] but pmap() does not exist
> yet. map() is all by all. That's the downside of it.
>
>
> On Fri, Mar 21, 2014 at 11:49 AM, nimrod.rubinstein <
> nimrod.rubinstein@gmail.com> wrote:
>
>> I guess I thought that map only maps ranges[x] with grangeslist[x] for
>> every x. Do I understand you correctly that it rather maps all ranges
>> against all grangeslist?
>>
>>
>> On Fri, Mar 21, 2014 at 2:39 PM, Michael Lawrence <
>> lawrence.michael@gene.com> wrote:
>>
>>>
>>>
>>>
>>> On Fri, Mar 21, 2014 at 11:29 AM, nimrod.rubinstein <
>>> nimrod.rubinstein@gmail.com> wrote:
>>>
>>>> Thanks for the help.
>>>>
>>>> Correct me if I'm wrong but it seems that I first intersect the
>>>> GAlignments with the GRangesList using the findSpliceOverlaps function, and
>>>> then run the map function where the granges are of the compatible GAlignments
>>>> and grangeslist is the corresponding list of GRanges from GRangesList.
>>>>
>>>> Makes sense?
>>>>
>>>>
>>> That will not quite work, you will always have to filter the results
>>> from the map() call, because it may try to map things that are not
>>> compatible.
>>>
>>>
>>>>
>>>> On Fri, Mar 21, 2014 at 2:20 PM, Michael Lawrence <
>>>> lawrence.michael@gene.com> wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Mar 21, 2014 at 10:56 AM, Cook, Malcolm <MEC@stowers.org>wrote:
>>>>>
>>>>>> Michael,
>>>>>>
>>>>>> +1 for pmap!
>>>>>>
>>>>>> I like the separation of concerns this would offer.
>>>>>>
>>>>>> I seems to me that the combination of pmap and findSpliceOverlaps
>>>>>> should afford a more general solution to the problem solved by
>>>>>> VariantAnnotation:: refLocsToLocalLocs  (and  should be equally
>>>>>> performant?).
>>>>>>
>>>>>>
>>>>> Yea, actually both map and refLocsToLocalLocs rely on the same
>>>>> underlying function for speed: GenomicRanges:::.listCumsumShifted (writing
>>>>> that one gave me a headache).
>>>>>
>>>>> Unfortunately I don't have the time to spend on things like pmap but I
>>>>> would encourage someone in Seattle to take it on. There's already a method
>>>>> for Ranges,GAlignments but that's the opposite direction as requested in
>>>>> this thread. I write these things as they come up in my work.
>>>>>
>>>>> ~Malcolm
>>>>>>
>>>>>>  >-----Original Message-----
>>>>>>  >From: bioconductor-bounces@r-project.org [mailto:
>>>>>> bioconductor-bounces@r-project.org] On Behalf Of Michael Lawrence
>>>>>>  >Sent: Friday, March 21, 2014 12:17 PM
>>>>>>  >To: rubi [guest]
>>>>>>  >Cc: GenomicRanges Maintainer; bioconductor@r-project.org;
>>>>>> nimrod.rubinstein@gmail.com
>>>>>>  >Subject: Re: [BioC] Obtain overlap coordinates in GenomicRanges
>>>>>> findSpliceOverlaps
>>>>>>  >
>>>>>>  >Currently there is
>>>>>>  >
>>>>>>  >m <- map(granges, grangeslist)
>>>>>>  >
>>>>>>  >Where 'm' is a RangesMapping indicating the within overlaps (Hits)
>>>>>> and the
>>>>>>  >mapped ranges. You would get the granges from the GAlignments with
>>>>>> the
>>>>>>  >granges() function. The problem is that the overlap computation uses
>>>>>>  >findOverlaps(type="within") instead of findSpliceOverlaps. One idea
>>>>>> would
>>>>>>  >be to take a Hits object as an optional argument. Or, we could add
>>>>>> a "pmap"
>>>>>>  >method that would assume the from and to are matched up already and
>>>>>> simply
>>>>>>  >perform the mapping.
>>>>>>  >
>>>>>>  >One quick fix would be to create a granges that consists a width-1
>>>>>> range at
>>>>>>  >the start position (and likewise the end position) for each read
>>>>>> and pass
>>>>>>  >it to map() as above. Then filter the mappings based on the
>>>>>> compatibility
>>>>>>  >results from findSpliceOverlaps(). Not that pretty nor very
>>>>>> efficient but
>>>>>>  >it takes care of the nasty stuff.
>>>>>>  >
>>>>>>  >Michael
>>>>>>  >
>>>>>>  >
>>>>>>  >
>>>>>>  >On Fri, Mar 21, 2014 at 9:44 AM, rubi [guest] <
>>>>>> guest@bioconductor.org>wrote:
>>>>>>  >
>>>>>>  >>
>>>>>>  >> Hi,
>>>>>>  >>
>>>>>>  >> I was wondering whether it is possible in anyway to obtain the
>>>>>> overlap
>>>>>>  >> coordinates when intersecting GAlignments objects as query with a
>>>>>>  >> GRangesList object, using the findSpliceOverlaps function?
>>>>>>  >>
>>>>>>  >> Specifically, I would like to obtain the transcriptomic
>>>>>> coordinates of the
>>>>>>  >> GAlignments in the transcripts that they compatibly intersect
>>>>>> with.
>>>>>>  >>
>>>>>>  >> Right now I'm obtaining this information in a 2 step approach:
>>>>>>  >> 1. findSpliceOverlaps(GAlignments, GRangesList,
>>>>>> ignore.strand=FALSE)
>>>>>>  >> 2. Keeping only the hits that are compatible, I then intersect
>>>>>> again each
>>>>>>  >> GAlignment and the ranges of the compatible GRange transcript and
>>>>>> sum the
>>>>>>  >> widths of the exons up to the intersection coordinate.
>>>>>>  >>
>>>>>>  >> My problem is that the second step is extremely slow.
>>>>>>  >>
>>>>>>  >> I'd be grateful for some discussion
>>>>>>  >>
>>>>>>  >>  -- output of sessionInfo():
>>>>>>  >>
>>>>>>  >> R version 3.0.2 (2013-09-25)
>>>>>>  >> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>>>  >>
>>>>>>  >> locale:
>>>>>>  >>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>>>  >>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>>>  >>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>>>>  >>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>>>>  >>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>>>>  >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>>>  >>
>>>>>>  >> attached base packages:
>>>>>>  >> [1] parallel  stats     graphics  grDevices utils     datasets
>>>>>>  methods
>>>>>>  >> [8] base
>>>>>>  >>
>>>>>>  >> other attached packages:
>>>>>>  >> [1] hash_2.2.6           data.table_1.8.10    Rsamtools_1.14.3
>>>>>>  >> [4] Biostrings_2.30.1    GenomicRanges_1.14.4 XVector_0.2.0
>>>>>>  >> [7] IRanges_1.20.6       BiocGenerics_0.8.0
>>>>>>  >>
>>>>>>  >> loaded via a namespace (and not attached):
>>>>>>  >> [1] bitops_1.0-6   stats4_3.0.2   tools_3.0.2    zlibbioc_1.8.0
>>>>>>  >>
>>>>>>  >>
>>>>>>  >> --
>>>>>>  >> Sent via the guest posting facility at bioconductor.org.
>>>>>>  >>
>>>>>>  >> _______________________________________________
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>>>>>>  >> Bioconductor@r-project.org
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>>>>>>  >> Search the archives:
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>>>>>>  >>
>>>>>>  >
>>>>>>  >      [[alternative HTML version deleted]]
>>>>>>  >
>>>>>>  >_______________________________________________
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>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>

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