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dynverse / dynmethods

A collection of 50+ trajectory inference methods within a common interface 📥📤
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URD #18

Closed zouter closed 6 years ago

zouter commented 6 years ago

https://github.com/farrellja/URD

zouter commented 6 years ago

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!