Closed ALSL2022 closed 2 years ago
Step 1: Probably you did it but, check for "NA" values in your data and remove them.
Step 2: Pass the data as a dataframe, not a tibble. I found that pathfindR
doesn't like the tibble class.
smth like:
DE_input %>% as.data.frame %>% run_pathfindR(convert2alias = FALSE, gene_sets = "Custom", custom_genes = mmu_kegg_genes, custom_descriptions = mmu_kegg_descriptions, pin_name_path = path2SIF)
I hope you can solve your problem with the instructions above.
Step 1: Probably you did it but, check for "NA" values in your data and remove them. Step 2: Pass the data as a dataframe, not a tibble. I found that
pathfindR
doesn't like the tibble class. I hope you can solve your problem with the instructions above.
Thank you very much! It worked perfectly when I converted to dataframe
Hi,
I am trying to use pathfindR on my dataset consisting of "differentially expressed" proteins (mouse), but when I run the function, I get the error "p values must all be numeric", even though it seems as if they already are?
My data:
head(DE_input)
sapply(DE_input,class)
The code:
DE_output <- run_pathfindR(input = DE_input, convert2alias = FALSE, gene_sets = "Custom", custom_genes = mmu_kegg_genes, custom_descriptions = mmu_kegg_descriptions, pin_name_path = path2SIF)
The error:
Error in pathfindR::input_testing(input, p_val_threshold) : p values must all be numeric
If I use the "built-in" data set "RA_input", everything works, so I guess something is wrong with my data set - do you have any idea, what I'm doing wrong?