pathfindR (version 1.3.0)

fuzzy_pw_clustering: Heuristic Fuzzy Multiple-linkage Partitioning of Pathways

Description

Heuristic Fuzzy Multiple-linkage Partitioning of Pathways

Usage

fuzzy_pw_clustering(kappa_mat, enrichment_res, kappa_threshold = 0.35,
  use_names = FALSE)

Arguments

kappa_mat

matrix of kappa statistics (output of `create_kappa_matrix`)

enrichment_res

data frame of pathway enrichment results

kappa_threshold

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

use_names

boolean to indicate whether to use pathway names instead of IDs (default = FALSE, i.e. use IDs)

Value

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

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

# NOT RUN {
fuzzy_pw_clustering(kappa_mat, enrichment_res)
fuzzy_pw_clustering(kappa_mat, enrichment_res, kappa_threshold = 0.45)
# }