| example_pathfindR_output_clustered {pathfindR.data} | R Documentation |
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 example_pathfindR_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").
Generated on 27 Apr 2024.
Usage
example_pathfindR_output_clustered
Format
A data frame with 121 rows and 11 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
- support
the median support (proportion of active subnetworks leading to enrichment within an iteration) over all iterations
s
- 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
example_pathfindR_input for the RA differentially-expressed genes data frame
example_experiment_matrix for the RA differentially-expressed genes expression matrix
run_pathfindR for details on the pathfindR enrichment analysis
example_pathfindR_output for the RA example pathfindR enrichment output
cluster_enriched_terms for details on clustering methods