Problem with interpreting output from Monocle3 graph_test()
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Entering edit mode
18 months ago
Angelina_G ▴ 10

Hello, I'm currently trying to look for trajectory analysis from my dataset and pseudotime analysis, I'm trying to look for the genes that contribute more significantly to the pseudotime calculation since they might be of interesting biological significance.

I tried with Monocle3, copying the workflow from the tutorial: https://cole-trapnell-lab.github.io/monocle3/docs/differential/

However, not that I've got the output, I find difficulty in understanding what information it has given me and how could I make better use of the analytical result (or just checking whether it's confidence level is sufficient). I understand that what I've got from the graph_test() is a list of genes, and (probably) their pseudotime related information. However, the only column I understand is that the first column is the list of genes... Could someone please help me understand what the other columns indicate? Like the p_value seems understandable and is an indication on statistical significance but I'm not sure what statistic it's telling me about and what comparison is it making...

Thank you so much!

example output from graph_test() after importing into csv

trajectory_analysis Monocle3 • 699 views
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Entering edit mode
3 months ago
abiuma ▴ 30

Hi, Did you find an answer for this?

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