create_jaccard_matrix: Compute the overlap matrix for enrichment results

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

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)

federicomarini/GeneTonic documentation built on Dec. 21, 2024, 10:05 p.m.