[BioC] distanceToNearest for GRanges?
Janet Young
jayoung at fhcrc.org
Tue Mar 27 19:36:22 CEST 2012
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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