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Question: From RleList to RleArray
2
gravatar for davide risso
17 days ago by
davide risso500
Weill Cornell Medicine
davide risso500 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 17 days ago by Peter Hickey290 • written 17 days ago by davide risso500
4
gravatar for Peter Hickey
17 days ago by
Peter Hickey290
Johns Hopkins University, Baltimore, USA
Peter Hickey290 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 17 days ago by Peter Hickey290

Thanks Pete!

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

ADD REPLYlink written 17 days ago by davide risso500
1

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

ADD REPLYlink written 16 days ago by Peter Hickey290

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

ADD REPLYlink written 3 days ago by Hervé Pagès ♦♦ 13k
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