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Question: From RleList to RleArray
2
gravatar for davide risso
11 weeks ago by
davide risso630
Weill Cornell Medicine
davide risso630 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 weeks ago by Peter Hickey320 • written 11 weeks ago by davide risso630
4
gravatar for Peter Hickey
11 weeks ago by
Peter Hickey320
Johns Hopkins University, Baltimore, USA
Peter Hickey320 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 weeks ago by Peter Hickey320

Thanks Pete!

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

ADD REPLYlink written 11 weeks ago by davide risso630
1

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

ADD REPLYlink written 11 weeks ago by Peter Hickey320

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

ADD REPLYlink written 9 weeks ago by Hervé Pagès ♦♦ 13k
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