[Bioc-devel] How to speed up GRange comparision

poverlaps()?

On Wed, Jan 29, 2020 at 7:50 AM web working <webworking at 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