[BioC] distanceToNearest for GRanges?

[Valerie Obenchain]

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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