[BioC] distanceToNearest for GRanges?

[Cook, Malcolm]

thanks Valerie,

Did you happen to vet the logic of my implementation, or did you just code it lower level from first principals?

Cheers,

~Malcolm

> -----Original Message-----
> From: Valerie Obenchain [mailto:vobencha at fhcrc.org]
> Sent: Wednesday, April 11, 2012 11:13 AM
> To: Janet Young
> Cc: Cook, Malcolm; bioconductor at r-project.org
> Subject: Re: [BioC] distanceToNearest for GRanges?
> 
> 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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