get_enriched_go() which is just a convenient wrapper around goseq::goseq. This has had minimal changes from Tom's notebook version.
estimate_go_overrep() which takes the output of get_enriched_go() and adds a column with estimated GO overrepresentation scores. I completely re-wrote this function so it runs a
lot faster, but the algorithm for calculating the score remains the same.
remove_redundant_go() which takes the output of get_enriched_go() and removes 'redundant' GO terms. This has had minimal changes from Tom's notebook version.
All three functions have Roxygen2 documentation, but no examples or tests (currently). These can be added in future PRs.
This PR adds some more of Tom's GO functions.
Specifically:
get_enriched_go()which is just a convenient wrapper aroundgoseq::goseq. This has had minimal changes from Tom's notebook version.estimate_go_overrep()which takes the output ofget_enriched_go()and adds a column with estimated GO overrepresentation scores. I completely re-wrote this function so it runs a lot faster, but the algorithm for calculating the score remains the same.remove_redundant_go()which takes the output ofget_enriched_go()and removes 'redundant' GO terms. This has had minimal changes from Tom's notebook version.All three functions have Roxygen2 documentation, but no examples or tests (currently). These can be added in future PRs.