richCluster (version 1.0.2)

david_cluster: Cluster Terms using DAVID's method

Description

This function performs clustering on enrichment results using an algorithm inspired by DAVID's functional clustering method.

Usage

david_cluster(
  enrichment_results,
  df_names = NULL,
  similarity_threshold = 0.5,
  initial_group_membership = 3,
  final_group_membership = 3,
  multiple_linkage_threshold = 0.5
)

Value

A named list containing the clustering results.

Arguments

enrichment_results

A list of dataframes, each containing enrichment results. Each dataframe should include at least the columns 'Term', 'GeneID', and 'Padj'.

df_names

Optional, a character vector of names for the enrichment result dataframes. Must match the length of `enrichment_results`. Default is `NULL`.

similarity_threshold

A numeric value for the kappa score cutoff (0 < cutoff <= 1).

initial_group_membership

Minimum number of terms to form an initial seed group.

final_group_membership

Minimum number of terms for a final cluster.

multiple_linkage_threshold

A numeric value for the merging threshold.