Combined_res question

[daacarri]

In the vignette a data frame called combined_res is made by combining itself with current_res, right before visualization. However it’s not clear on what is being combined as that data frame is not made anywhere else in the code. Is it a typo and are you suppose to combine with the data frame made right before current_res? I tried and got a character length error. I also tried with just the current res df and got results but only 4 genes contributed. Not sure if that’s a typo in the vignette or what.

[egeulgen]

I'm assuming you meant the Step-by-Step Execution vignette.

Have you encountered any issues with run_pathfindR()? We generally suggest using this wrapper function instead of manually performing the steps.

In the vignette, the combined_res dataframe is used to store the result of each iteration and is created right before the loop (combined_res <- NULL). Within the loop, each iteration's result (stored in current_res) is added to the combined_res.

Let me know if this helps,
Best,
-E

[daacarri]

I have it now, thanks. However, it only returned 4 distinct genes (and their subsequent pathways). What are the odds only 4 genes/pathways would be returned?

[egeulgen]

Depending on the size of your input genes, yes it is possible