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Question: From RleList to RleArray
2
gravatar for davide risso
11 months ago by
davide risso750
Weill Cornell Medicine
davide risso750 wrote:

Hi all,

is there a way to transform an RleList (or a list of Rle's) into a RleArray / RleMatrix?

My use case is that I have a loop / lapply that returns a list of Rle objects that I would like to store as a RleMatrix (each column as an Rle).

Minimal example:

x <- Rle(10:1, 1:10)
rl <- RleList(x, x)

Ideally, something like

rm <- RleArray(rl, dim=c(length(x), length(r1))

or

rm <- as(rl, "RleArray")

The more realistic (but not reproducible at this moment example):

idx <- c(50, 100)
rleBinCovList <- lapply(idx, function(win) {
        runsum(chrCovRle, k=win, endrule="constant")
    })

Or perhaps is there a way to create directly a RleArray?

Thanks! Davide

ADD COMMENTlink modified 11 months ago by Peter Hickey380 • written 11 months ago by davide risso750
4
gravatar for Peter Hickey
11 months ago by
Peter Hickey380
Johns Hopkins University, Baltimore, USA
Peter Hickey380 wrote:

rm <- RleArray(unlist(rl), c(lengths(rl)[1], length(rl))) will give you what you want (the unlist() is cheap because of how an RleList is defined). With some checks added, this could become the as(rl, "RleArray") method.

ADD COMMENTlink written 11 months ago by Peter Hickey380

Thanks Pete!

I knew you could help! I almost just wrote directly to you ;)

ADD REPLYlink written 11 months ago by davide risso750
1

Will try to write a PR to add this to DelayedArray over the next few days

ADD REPLYlink written 11 months ago by Peter Hickey380

Thanks for the PR Pete. I just merged it.  H.

ADD REPLYlink written 11 months ago by Hervé Pagès ♦♦ 13k
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