Avoids error in remove_redundant_go when GO term has no ontology

CambridgeCentreForProteomics / camprotR

https://cambridgecentreforproteomics.github.io/camprotR/

MIT License

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Avoids error in remove_redundant_go when GO term has no ontology #25

Closed TomSmithCGAT closed 2 years ago

TomSmithCGAT commented 2 years ago

Small debug.

As per get_ancestor_go, in remove_redundant_go, we need to catch instances where the GO term does not match to an ontology, since this throws an error downstream.

Copied the same lines from above function. Could consider re-factoring code to include a get_ontologies function.

csdaw commented 2 years ago

Apologies, I'm going to co-opt this PR and add some tests for the GO enrichment functions. For now I've just added a small data.frame with the results of a differential enrichment analysis (i.e. UniProt accessions, p-values, etc...) which I'll use to test get_enriched_go() and friends.

TomSmithCGAT commented 2 years ago

That's great. I've got another plotting function to add sitting on a separate branch so I'll add that here instead.

csdaw commented 2 years ago

I think there is a Windows-specific error with my GO tests so I'll have to try it on my Windows laptop at home.

csdaw commented 2 years ago

This rather large PR (in hindsight it is better to keep them small and merge quickly) now includes the following:

Add tests for most GO functions
Add plot_go() function for plotting GO enrichment results quickly
Add dep_gene2cat dataset which is used for speeding up GO tests, and can be used as an example in vignettes etc.
Minor addition to remove_redundant_go() to catch instances where the GO term does not match to an ontology
Minor edits to GO function docs