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HectorRDB / condiments

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
https://hectorrdb.github.io/condiments/
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Out put of the topology test for multiple comparisons #10

Closed ghost closed 2 years ago

ghost commented 2 years ago

Hi Hector, Thank you for the wonderful package! I am not very familiar with the "classifier" method used in topology test. However, I wonder if the output could include p-value for multiple comparions. I have four conditions which I expect condition A and B look similar whereas condition C and D resemble each other but differ from A and B. The output of the topology test rejects the null hypothesis so I think my theory might be right. Now I'm curious if the stats supports that they are seggregated into two groups. Any suggestions or comments will be really appreciated!

HectorRDB commented 2 years ago

Hi @rtoddler in the topologyTest, there are no options for doing pairwise comparisons. If you think the pairings should be A-B and C-D, I would just run the topologyTest on just A-B and then just C-D separately to validate this. Unfortunately, correcting for multiple testing optimally would be a bit tricky given how correlated each test is but that should give you a grounding to support your hypothesis.

Hope that helps, let me know if you need anything else

ghost commented 2 years ago

Hi @HectorRDB Thank you for your suggestion! I encountered another problem with downloading data from KRAS. Please see the log below. Thanks! Error: Join columns must be present in data. x Problem with X1. Run rlang::last_error() to see where the error occurred.

rlang::last_error() <error/rlang_error> Join columns must be present in data. x Problem with X1. Backtrace:

  1. condimentsPaper::import_KRAS()
  2. dplyr:::full_join.data.frame(celltype, pst, by = "X1")
  3. dplyr:::join_mutate(...)
  4. dplyr:::join_cols(...)
  5. dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
  6. dplyr:::check_join_vars(by$x, x_names) Run rlang::last_trace() to see the full context. rlang::last_trace() <error/rlang_error> Join columns must be present in data. x Problem with X1. Backtrace: x
  7. -condimentsPaper::import_KRAS()
  8. +-dplyr::full_join(celltype, pst, by = "X1")
  9. -dplyr:::full_join.data.frame(celltype, pst, by = "X1")
  10. -dplyr:::join_mutate(...)
  11. -dplyr:::join_cols(...)
  12. -dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
  13. -dplyr:::check_join_vars(by$x, x_names)
HectorRDB commented 2 years ago

Thanks for reporting, that function might not be up to date. I'll check it out. In the meantime, the KRAS data can loaded with data("kras", package = "condimentsPaper")