Question: From RleList to RleArray
2
gravatar for davide risso
2.1 years ago by
davide risso830
University of Padova
davide risso830 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

rle rlelist delayedarray • 604 views
ADD COMMENTlink modified 2.1 years ago by Peter Hickey460 • written 2.1 years ago by davide risso830
Answer: From RleList to RleArray
4
gravatar for Peter Hickey
2.1 years ago by
Peter Hickey460
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Peter Hickey460 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 2.1 years ago by Peter Hickey460

Thanks Pete!

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

ADD REPLYlink written 2.1 years ago by davide risso830
1

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

ADD REPLYlink written 2.1 years ago by Peter Hickey460

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

ADD REPLYlink written 2.1 years ago by Hervé Pagès ♦♦ 14k
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