[Bioc-devel] How to speed up GRange comparision

[Jianhong Ou, Ph.D.]

Oh, I forget that. Thank you for reminder. 
Then how about:

distance(query, narrow(subject, start=2, end=-2)) == 0

?


On 1/29/20, 12:40 PM, "Pages, Herve" <hpages using fredhutch.org> wrote:

    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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