Simplify results from functional enrichment analysis, removing genesets that are redundant to enhance interpretation of the results
gs_simplify(res_enrich, gs_overlap = 0.75)A data.frame object, storing the result of the functional
enrichment analysis. See more in the main function, GeneTonic(), to check the
formatting requirements (a minimal set of columns should be present).
Numeric value, which defines the threshold for removing
terms that present an overlap greater than the specified value. Changing its
value can control the granularity of how redundant terms are removed from the
original res_enrich for the next steps, e.g. plotting this via gs_volcano()
A data.frame with a subset of the original gene sets
gs_volcano() and ggs_graph() can e.g. show an overview on the
simplified table of gene sets
# res_enrich object
data(res_enrich_macrophage, package = "GeneTonic")
res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)
#> Found 500 gene sets in `topGOtableResult` object.
#> Converting for usage in GeneTonic...
dim(res_enrich)
#> [1] 500 7
res_enrich_simplified <- gs_simplify(res_enrich)
dim(res_enrich_simplified)
#> [1] 143 7
# and then use this further for all other functions expecting a res_enrich