create_jaccard_matrix {GeneTonic} | R Documentation |
Compute the overlap matrix for enrichment results, based on the Jaccard Index between each pair of sets
create_jaccard_matrix( res_enrich, n_gs = nrow(res_enrich), gs_ids = NULL, return_sym = FALSE )
res_enrich |
A |
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
|
gs_ids |
Character vector, containing a subset of |
return_sym |
Logical, whether to return the symmetrical matrix or just the
upper triangular - as needed by |
A matrix with the kappa scores between gene sets
# 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)