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Question: From RleList to RleArray
2
gravatar for davide risso
8 months ago by
davide risso740
Weill Cornell Medicine
davide risso740 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 8 months ago by Peter Hickey370 • written 8 months ago by davide risso740
4
gravatar for Peter Hickey
8 months ago by
Peter Hickey370
Johns Hopkins University, Baltimore, USA
Peter Hickey370 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 8 months ago by Peter Hickey370

Thanks Pete!

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

ADD REPLYlink written 8 months ago by davide risso740
1

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

ADD REPLYlink written 8 months ago by Peter Hickey370

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

ADD REPLYlink written 8 months ago by Hervé Pagès ♦♦ 13k
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