miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance

Question

[shuaizh117]

I was trying to run "milo.PH <- calcNhoodDistance(milo.PH, d=25, reduced.dim = "HARMONY")", and it's been running without giving any error, however, when I click on STOP, it gave the error as

"Error in get(as.character(FUN), mode = "function", envir = envir) :
object 'as.SimpleList' of mode 'function' was not found"

All previous steps work fine as below:

sce<- as.SingleCellExperiment(PH.lung.sct)
#create a milo object
milo.PH <- Milo(sce)
#construct KNN graph
milo.PH <- buildGraph(milo.PH, k = 30, d = 25, reduced.dim = "HARMONY")
#Defining representative neighborhoods on the KNN graph
milo.PH <- makeNhoods(milo.PH, prop = 0.05, k = 30, d=25, refined = TRUE, reduced_dims = "HARMONY")
plotNhoodSizeHist(milo.PH)
#Counting cells in neighbourhoods
milo.PH <- countCells(milo.PH, meta.data = as.data.frame(colData(milo.PH)), sample="patient")
head(nhoodCounts(milo.PH))

Any suggestions or comments would be appreciated!

[filippo.costa]

I'm running into the same error, did you manage to find a solution?

Answer 1

[michael.morgan]

FYI - this didn't get tagged as miloR, so it didn't come up on my radar.

First thing is, hopefully you aren't still having a problem. Secondly, the calcNhoodDistance function is pretty much deprecated now in favour of the graph-only approach described in Kluzer et al. You can get this using makeNoods(..., refinement_scheme="graph") and testNhoods(..., fdr.weighting="graph-overlap").