[BioC] distanceToNearest for GRanges?

[Valerie Obenchain]

This has been added to GenomicRanges 1.9.4. You will also need IRanges 
1.15.2.

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
>>>
>>>
>>> -------------------------------------------------------------------
>>>
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