Entering edit mode
Hi all,
Suppose I've created a Hits object by
all_hits <- findOverlaps(query, subject, select = 'all', type = 'any')
and now I want to get the first (or last) hit for each query. Of
course, I could use
first_hits <- findOverlaps(query, subject, select = 'first', type =
'any')
last_hits <- findOverlaps(query, subject, select = 'last', type =
'any')
but I this isn't necessary as all the required information is in the
all_hits Hits object.
I was unable to find a function to do what I wanted, however, based at
the source for findOverlaps-methods.R (actually Hector's branch at
https://github.com/hcorrada/GenomicRanges/blob/master/R/findOverlaps-
methods.R) I wrote the following simple functions
getFirstHit <- function(all_hits){
ans <- rep.int(NA_integer_, queryLength(all_hits))
oo <- IRanges:::orderIntegerPairs(queryHits(all_hits),
subjectHits(all_hits), decreasing = TRUE)
ans[queryHits(all_hits)[oo]] <- subjectHits(all_hits)[oo]
return(ans)
}
getLastHit <- function(all_hits){
ans <- rep.int(NA_integer_, queryLength(all_hits))
ans[queryHits(all_hits)] <- subjectHits(all_hits)
return(ans)
}
These do what I want and are faster than re-running findOverlaps for
my use case (millions of query intervals with tens of thousands of
subject intervals)
Now to my questions:
(1) Did I just overlook built-in "getFirstHit" and "getLastHit"
functions?
(2) Would others find "getFirstHit" and "getLastHit" useful enough to
justify their inclusion in GenomicRanges (or IRanges, wherever it
belongs)?
(3) I recall some discussion on this mailing list and Rdevel stating
that using ":::" to access non-exported functions isn't a great idea
for use in package code. If I need to include my own "getFirstHit"
would someone be so kind as to point me to the best advice for
avoiding calls to ":::" in my code to access
IRanges:::orderIntegerPairs(queryHits)?
Many thanks,
Pete
--------------------------------
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324
hickey@wehi.edu.au
http://www.wehi.edu.au
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