[Bioc-devel] How to speed up GRange comparision

[Michael Lawrence]

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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-- 
Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla using gene.com

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