pathfindR (version 2.3.1)

fuzzy_term_clustering: Heuristic Fuzzy Multiple-linkage Partitioning of Enriched Terms

Description

Heuristic Fuzzy Multiple-linkage Partitioning of Enriched Terms

Usage

fuzzy_term_clustering(
  kappa_mat,
  enrichment_res,
  kappa_threshold = 0.35,
  use_description = FALSE
)

Value

a boolean matrix of cluster assignments. Each row corresponds to an enriched term, each column corresponds to a cluster.

Arguments

kappa_mat

matrix of kappa statistics (output of create_kappa_matrix)

enrichment_res

data frame of pathfindR enrichment results. Must-have columns are 'Term_Description' (if use_description = TRUE) or 'ID' (if use_description = FALSE), 'Down_regulated', and 'Up_regulated'. If use_active_snw_genes = TRUE, 'non_Signif_Snw_Genes' must also be provided.

kappa_threshold

threshold for kappa statistics, defining strong relation (default = 0.35)

use_description

Boolean argument to indicate whether term descriptions (in the 'Term_Description' column) should be used. (default = FALSE)

Details

The fuzzy clustering algorithm was implemented based on: Huang DW, Sherman BT, Tan Q, et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 2007;8(9):R183.

Examples

if (FALSE) {
fuzzy_term_clustering(kappa_mat, enrichment_res)
fuzzy_term_clustering(kappa_mat, enrichment_res, kappa_threshold = 0.45)
}