[BioC] distanceToNearest for GRanges?

[Janet Young]

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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>