Compute the kappa matrix for enrichment results

Source: R/gs_distances.R

Compute the kappa matrix for enrichment results, as a measure of overlap

create_kappa_matrix(
  res_enrich,
  gtl = NULL,
  n_gs = nrow(res_enrich),
  gs_ids = NULL
)

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.

Value

A matrix with the kappa scores between gene sets

See also

gs_mds()

Examples


# 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...

kmat <- create_kappa_matrix(res_enrich[1:200, ])
dim(kmat)
#> [1] 200 200