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No2Ross / TrAGEDy

Trajectory Alignment of Gene Expression Dynamics
MIT License
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Slingshot pseudotime NA values #3

Open zhangol opened 1 year ago

zhangol commented 1 year ago

Hi, I tried to useTrAGEDy, the I performed analysis on the dataset and generate two trajectories, when I used the TrAGEDY to compare the two lines, I found the NA of the pseudotime will affect the code running, then I use the pseudotime <- slingPseudotime(sce, na = FALSE), However, I try to find optimal path, it throws me the error. Can I use the TrAGEDy to compare the two trajectories in one dataset. And should I use the same counts matrix for the two trajectories?

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No2Ross commented 1 year ago

Hi Mingfeng,

You certainly could use TrAGEDy to compare the trajectories in the same dataset, however I imagine it will just show the two beginning the same and then diverging (like the pseudotime does).

When I ran into NA values, i've subsetted out cells that are only present on the trajectory lineage of interest to me, meaning no NA value cells are left when TrAGEDy is performed.

Next week we can talk about it in person if you are still having trouble.

Ross

No2Ross commented 1 year ago

Hi Mingfeng,

I'm at a conference today and yesterday, so it would have to be tomorrow or Thursday. Does that work for you?

Best wishes, Ross