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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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go_all_genes_description file is not found #27

Closed boseb closed 4 years ago

boseb commented 4 years ago

Hi, I am trying to do single gene set enrichment with GO using enrichment( input_genes, genes_by_term = pathfindR::go_all_genes, term_descriptions = GO_all_terms_df, adj_method = "bonferroni", enrichment_threshold = 0.05, sig_genes_vec, background_genes=unlist(go_all_genes) )

It seems description file "GO_all_terms_df" is missing. Please help. Thanks Bose

egeulgen commented 4 years ago

hey @boseb,

that data frame is an internal object so you can only access it via pathfindR:::GO_all_terms_df. However, that is not the term descriptions in the correct format so it needs to be processed as a named vector.

If you want to perform simple ORA using input_genes on "GO-All", you should follow below:

library(pathfindR)
go_df <- pathfindR:::GO_all_terms_df
go_all_descriptions <- go_df$GO_term
names(go_all_descriptions) <- go_df$GO_ID

result_df <- enrichment(input_genes = input_genes,
                        genes_by_term = go_all_genes,
                        term_descriptions = go_all_descriptions,
                        adj_method = "bonferroni", # default
                        enrichment_threshold = 0.05, # default
                        sig_genes_vec = input_genes, # because you are only performing ORA
                        background_genes = unique(unlist(go_all_genes))) # or some other "universe" of background genes

Hope this helps, -E