[Bioc-devel] How to speed up GRange comparision

Jianhong Ou, Ph.D. j|@nhong@ou @end|ng |rom duke@edu
Wed Jan 29 17:04:37 CET 2020

dist=distance(query, subject)

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:

    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
    # 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]))
    # 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?
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