Comments (1)
Difficult to wrap, errors at different steps:
> floods <- floodPseudotime(urd, root.cells = c(start_id), n=1000, minimum.cells.flooded = 10, verbose=F)
Error in apply(tm.flood[cells.not.visited, cells.visited], 1, combine.probs) :
dim(X) must have a positive length
This is fixed in farrellja/URD#7
> ptlogistic <- pseudotimeDetermineLogistic(urd, "pseudotime", optimal.cells.forward=20, max.cells.back=40, do.plot = F)
Error in pseudotime.vec[1:(length(pseudotime.vec) - max.cells.back)] :
only 0's may be mixed with negative subscripts
This is probably caused by NAs in the pseudotime, but hard to see how they get there
> urd@pseudotime
pseudotime
C1 NA
C2 NA
C3 NA
C4 NA
C5 NA
C6 NA
C7 NA
C8 NA
Perhaps @farrellja can chime in? Would be great to have your method included!
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