create_kappa_matrix: Compute the kappa matrix for enrichment results

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

Compute the kappa matrix for enrichment results

Description

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

Usage

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)

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

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