fuzzy_term_clustering | R Documentation |
Heuristic Fuzzy Multiple-linkage Partitioning of Enriched Terms
fuzzy_term_clustering(
kappa_mat,
enrichment_res,
kappa_threshold = 0.35,
use_description = FALSE
)
kappa_mat |
matrix of kappa statistics (output of |
enrichment_res |
data frame of pathfindR enrichment results. Must-have
columns are 'Term_Description' (if |
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 = |
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.
a boolean matrix of cluster assignments. Each row corresponds to an enriched term, each column corresponds to a cluster.
## Not run:
fuzzy_term_clustering(kappa_mat, enrichment_res)
fuzzy_term_clustering(kappa_mat, enrichment_res, kappa_threshold = 0.45)
## End(Not run)
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