create_jaccard_matrix {GeneTonic} | R Documentation

## Compute the overlap matrix for enrichment results

### Description

Compute the overlap matrix for enrichment results, based on the Jaccard Index between each pair of sets

### Usage

    create_jaccard_matrix(
      res_enrich,
      gtl = NULL,
      n_gs = nrow(res_enrich),
      gs_ids = NULL,
      return_sym = FALSE
    )

### Arguments

`res_enrich` | A `data.frame` object, storing the result of the functional enrichment analysis. See more in the main function, `GeneTonic()`, to see the formatting requirements.
`gtl` | A `GeneTonic`-list object, containing in its slots the arguments specified above: `dds`, `res_de`, `res_enrich`, and `annotation_obj` - the names of the list must be specified following the content they are expecting
`n_gs` | Integer value, corresponding to the maximal number of gene sets to be included (from the top ranked ones). Defaults to the number of rows of `res_enrich`
`gs_ids` | Character vector, containing a subset of `gs_id` as they are available in `res_enrich`. Lists the gene sets to be included, additionally to the ones specified via `n_gs`. Defaults to NULL.
`return_sym` | Logical, whether to return the symmetrical matrix or just the upper triangular - as needed by `enrichment_map()`, for example.

### Value

A matrix with the kappa scores between gene sets

### See Also

`gs_mds()`, `enrichment_map()`

### Examples

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

    jmat <- create_jaccard_matrix(res_enrich[1:200, ])
    dim(jmat)

[Package GeneTonic version 1.4.1 Index]