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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