Say I have Hits-object along these lines:

from <- c(5, 2, 3, 3, 3, 2)
to <- c(11, 15, 5, 4, 6, 11)

hits <- Hits(from, to, 7, 15, sort.by.query=TRUE)

For every hit, I can assign some value:

mcols(hits)$val <-  c(10, 11, 15, 12, 10, 10)

I then want to break all ties, similar to breakTies:

breakTies(hits, "first")

However, I don't just want to resolve ties by the index, but rather on the val-column in mcols, i.e. the maximum value so the output would look like this:

hits[c(2,3,6)]

Is there a smart way on doing this, without first coercing the Hits-object into a data.frame and then back?

You could aggregate like this:

idx <- which.max(splitAsList(mcols(hits)$val, queryHits(hits)), global=TRUE)
hits[idx]

Maybe we should support something like this?

breakTies(hits, select="last", rank=~val)

It would be easy to support.