[Bioc-devel] How to speed up GRange comparision

[Pages, Herve]

On 1/29/20 08:04, Jianhong Ou, Ph.D. wrote:
> Try
> dist=distance(query, subject)
> dist==0
> ?

Please be aware that dist==0 does NOT mean that 2 ranges overlap. It 
means that they overlap OR are **adjacent**:

 > distance(GRanges("chr1:1-20"), GRanges("chr1:21-25"))
[1] 0

H.

> 
> On 1/29/20, 10:50 AM, "Bioc-devel on behalf of web working" <bioc-devel-bounces using r-project.org on behalf of 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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> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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