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!
