compatibility with alabaster.sce and DelayedArray

[alikhuseynov]

Hi, I'm having issues when running milo workflow when count data is DelayedMatrix, is there compatibility with alabaster.sce and DelayedArray ?
This currently won't work:

library(alabaster.sce)
library(SingleCellExperiment)
library(miloR)
milo <- Milo(sce)
# save SCE with alabaster.sce
fsave <- file.path(out_dir, "milo_obj")
saveObject(milo, fsave)
rm(milo)
# read saved object
milo <- readObject(fsave)
milo <- buildGraph(milo, k = 20, d = 30, reduced.dim = "PCA")
Error: unable to find an inherited method for function ‘findKNN’ for signature ‘X = "DelayedMatrix"’

any suggestions?
Thanks

[MikeDMorgan]

Hi @alikhuseynov - the buildGraph function from Milo uses BiocNeighbors findKNN(), so you may want to double-check the compatability/versions you have installed for BiocNeighbours and DelayedArray data types.

[alikhuseynov]

Hi @MikeDMorgan, Thanks for getting back on this.
I have release versions:

package.version("BiocNeighbors")
[1] "2.0.1"
> package.version("DelayedArray")
[1] "0.32.0"

I was expecting that findKNN() would work on "DelayedMatrix" or "ReloadedMatrix" by default, apparently it doesn't. Or am I missing something?
thanks

[MikeDMorgan]

That's definitely a question for Aaron Lun as BiocNeighbors maintainer.