pathfindR (version 1.4.2)

RA_clustered: Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis

Description

A dataset containing the results of pathfindR's clustering and partitioning workflow performed on the rheumatoid arthritis enrichment results RA_output. The clustering and partitioning function cluster_enriched_terms was used with the default settings (i.e. hierarchical clustering was performed and the agglomeration method was "average"). The optimal number of clusters (yielding the highest average silhouette width) was determined to be 15 and the enriched terms with the lowest p values in each cluster were assigned as representative terms for those clusters. Generated on Nov 1, 2019.

Usage

RA_clustered

Format

A data frame with 95 rows and 10 columns:

ID

ID of the enriched term

Term_Description

Description of the enriched term

Fold_Enrichment

Fold enrichment value for the enriched term

occurrence

the number of iterations that the given term was found to enriched over all iterations

lowest_p

the lowest adjusted-p value of the given term over all iterations

highest_p

the highest adjusted-p value of the given term over all iterations

Up_regulated

the up-regulated genes in the input involved in the given term, comma-separated

Down_regulated

the down-regulated genes in the input involved in the given term, comma-separated

Cluster

the cluster to which the enriched term is assigned

Status

whether the enriched term is the "Representative" term in its cluster or only a "Member"

See Also

RA_input for the RA differentially-expressed genes data frame RA_clustered for the RA example pathfindR clustering output RA_exp_mat for the RA differentially-expressed genes expression matrix run_pathfindR for details on the pathfindR enrichment analysis RA_output for the RA example pathfindR enrinchment output cluster_enriched_terms for details on clustering methods