[Bioc-devel] How to speed up GRange comparision

[Pages, Herve]

Yes poverlaps().

Or pcompare(), which should be even faster. But only if you are not 
afraid to go low-level. See ?rangeComparisonCodeToLetter for the meaning 
of the codes returned by pcompare().

H.

On 1/29/20 08:01, Michael Lawrence via Bioc-devel wrote:
> poverlaps()?
> 
> On Wed, Jan 29, 2020 at 7:50 AM web working <webworking using posteo.de> wrote:
>>
>> Hello,
>>
>> I have two big GRanges objects and want to search for an overlap of  the
>> first range of query with the first range of subject. Then take the
>> second range of query and compare it with the second range of subject
>> and so on. Here an example of my problem:
>>
>> # GRanges objects
>> query <- GRanges(rep("chr1", 4), IRanges(c(1, 5, 9, 20), c(2, 6, 10,
>> 22)), id=1:4)
>> subject <- GRanges(rep("chr1",4), IRanges(c(3, 1, 1, 15), c(4, 2, 2,
>> 21)), id=1:4)
>>
>> # The 2 overlaps at the first position should not be counted, because
>> these ranges are at different rows.
>> countOverlaps(query, subject)
>>
>> # Approach 1 (bad style. I have simplified it to understand)
>> dat <- as.data.frame(findOverlaps(query, subject))
>> indexDat <- apply(dat, 1, function(x) x[1]==x[2])
>> indexBool <- dat[indexDat,1]
>> out <- rep(FALSE, length(query))
>> out[indexBool] <- TRUE
>> as.numeric(out)
>>
>> # Approach 2 (bad style and takes too long)
>> out <- vector("numeric", 4)
>> for(i in seq_along(query)) out[i] <- (overlapsAny(query[i], subject[i]))
>> out
>>
>> # Approach 3 (wrong results)
>> as.numeric(overlapsAny(query, subject))
>> as.numeric(overlapsAny(split(query, 1:4), split(subject, 1:4)))
>>
>>
>> Maybe someone has an idea to speed this up?
>>
>>
>> Best,
>>
>> Tobias
>>
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> 
> 
> 

-- 
Hervé Pagès

Program in Computational Biology
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