I forget to say thank you for this.  It's an exceptionally handy feature.

thanks,

--t


On Fri, Apr 20, 2012 at 10:07 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 04/20/2012 07:52 AM, Michael Muratet wrote:
>
>>
>> On Apr 11, 2012, at 11:12 AM, Valerie Obenchain wrote:
>>
>>  This has been added to GenomicRanges 1.9.4. You will also need IRanges
>>> 1.15.2.
>>>
>> Greetings
>>
>> I need this functionality, but I only see GenomicRanges version on the
>> Bioconductor site. I couldn't find it under the Developer links, either.
>> Is it available and where can I get it?
>>
>
> The modification is available in the 'devel' branch; instructions (a
> little complicated) are available at
>
> http://bioconductor.org/**developers/useDevel/<http://bioconductor.org/developers/useDevel/>
>
> Devel packages are summarized at
>
> http://bioconductor.org/**packages/devel/BiocViews.html<http://bioconductor.org/packages/devel/BiocViews.html>
>
> where the current GenomicRanges version is 1.9.7.
>
> Martin
>
>
>
>> Thanks
>>
>> Mike
>>
>>
>>> Valerie
>>>
>>>
>>> On 03/27/2012 10:36 AM, Janet Young wrote:
>>>
>>>> Hi,
>>>>
>>>> thank you both - very helpful.
>>>>
>>>> Janet
>>>>
>>>>
>>>>
>>>> On Mar 27, 2012, at 6:35 AM, Valerie Obenchain wrote:
>>>>
>>>>  Hi Janet, Malcom,
>>>>>
>>>>> Yes, we can add distanceToNearest for GRanges. This will probably
>>>>> happen after the release (i.e., next week). I'll post back here when
>>>>> it's complete.
>>>>>
>>>>> Valerie
>>>>>
>>>>>
>>>>> On 03/26/12 16:26, Cook, Malcolm wrote:
>>>>>
>>>>>> Janet,
>>>>>>
>>>>>> In the mean time....
>>>>>>
>>>>>> distanceToNearest.GRanges<- function
>>>>>> (query,subject=query,...,.AS=**DataFrame) {
>>>>>> ## PURPOSE: an implementation of distanceToNearest for GRanges in
>>>>>> ## terms of 'nearest' and 'distance' whose return value is shaped
>>>>>> ## like that of IRange's 'nearest', by default, but you can ask for
>>>>>> ## the result .AS=data.table or .AS=data.frame if you prefer.
>>>>>> if(missing(subject)) {
>>>>>> nearestSubjectIndex<-nearest(**query,...)
>>>>>> } else {
>>>>>> nearestSubjectIndex<-nearest(**query,subject,...)
>>>>>> }
>>>>>> queryHasNearest<-! is.na(nearestSubjectIndex)
>>>>>> queryIndex<-which(**queryHasNearest)
>>>>>> queryHavingNearest<-query[**queryIndex]
>>>>>> nearestSubjectIndex<-**nearestSubjectIndex[**queryIndex]
>>>>>> nearestSubject<-subject[**nearestSubjectIndex]
>>>>>> d<-distance(**queryHavingNearest,**nearestSubject)
>>>>>> .AS(query=queryIndex
>>>>>> ,subject=nearestSubjectIndex
>>>>>> ,distance=d)
>>>>>> }
>>>>>>
>>>>>> You've asked so many questions in this forum whose answer I made
>>>>>> use of that I must owe you this tidbit....
>>>>>>
>>>>>> Lurkers, and fellow travelers, I welcome corrections and stylistic
>>>>>> suggestions.
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Malcolm Cook
>>>>>>
>>>>>>
>>>>>> ______________________________**__________
>>>>>> From: bioconductor-bounces@r-**project.org<bioconductor-bounces@r-project.org>
>>>>>> [bioconductor-bounces@r-**project.org<bioconductor-bounces@r-project.org>]
>>>>>> On Behalf Of Janet Young
>>>>>> [jayoung@fhcrc.org]
>>>>>> Sent: Monday, March 26, 2012 4:42 PM
>>>>>> To: bioconductor@r-project.org
>>>>>> Subject: [BioC] distanceToNearest for GRanges?
>>>>>>
>>>>>> Hi there,
>>>>>>
>>>>>> Any plans to implement distanceToNearest for GRanges objects? That
>>>>>> would be really useful for me.
>>>>>>
>>>>>> thanks,
>>>>>>
>>>>>> Janet
>>>>>>
>>>>>>
>>>>>> ------------------------------**------------------------------**
>>>>>> -------
>>>>>>
>>>>>> Dr. Janet Young
>>>>>>
>>>>>> Tapscott and Malik labs
>>>>>>
>>>>>> Fred Hutchinson Cancer Research Center
>>>>>> 1100 Fairview Avenue N., C3-168,
>>>>>> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>>>>>>
>>>>>> tel: (206) 667 1471 fax: (206) 667 6524
>>>>>> email: jayoung ...at... fhcrc.org
>>>>>>
>>>>>>
>>>>>> ------------------------------**------------------------------**
>>>>>> -------
>>>>>>
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>>>>>>
>>>>>
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>>>
>>
>> Michael Muratet, Ph.D.
>> Senior Scientist
>> HudsonAlpha Institute for Biotechnology
>> mmuratet@hudsonalpha.org
>> (256) 327-0473 (p)
>> (256) 327-0966 (f)
>>
>> Room 4005
>> 601 Genome Way
>> Huntsville, Alabama 35806
>>
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>>
>
>
> --
> Computational Biology
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
>
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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