gs_simplify {GeneTonic} | R Documentation

## Simplify results from functional enrichment analysis

### Description

Simplify results from functional enrichment analysis, removing genesets that are redundant to enhance interpretation of the results

### Usage

    gs_simplify(res_enrich, gs_overlap = 0.75)

### Arguments

`res_enrich` | 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).
`gs_overlap` | 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()`

### Value

A `data.frame` with a subset of the original gene sets

### See Also

`gs_volcano()` and `ggs_graph()` can e.g. show an overview on the simplified table of gene sets

### Examples

    # res_enrich object
    data(res_enrich_macrophage, package = "GeneTonic")
    res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)

    dim(res_enrich)
    res_enrich_simplified <- gs_simplify(res_enrich)
    dim(res_enrich_simplified)
    # and then use this further for all other functions expecting a res_enrich

[Package GeneTonic version 1.0.1 Index]