[BioC] distanceToNearest for GRanges?

[Martin Morgan]

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/

Devel packages are summarized at

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 at r-project.org
>>>>> [bioconductor-bounces at r-project.org] On Behalf Of Janet Young
>>>>> [jayoung at fhcrc.org]
>>>>> Sent: Monday, March 26, 2012 4:42 PM
>>>>> To: bioconductor at 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
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
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>>>>> _______________________________________________
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>>
>> _______________________________________________
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>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
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>
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