| example_comparison_output {pathfindR.data} | R Documentation |
Second Example Output for the pathfindR Enrichment Workflow (H.sapiens. - Rheumatoid Arthritis data)
Description
The data frame containing the results of pathfindR's active-subnetwork-oriented
enrichment workflow performed on the rheumatoid arthritis dataset GSE84074
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84074. Analysis via
run_pathfindR was performed using the default settings.
Generated on 27 Apr 2024.
Usage
example_comparison_output
Format
A data frame with 38 rows and 9 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
- 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
See Also
example_pathfindR_input for the RA differentially-expressed genes data frame
example_pathfindR_output for the RA example pathfindR enrichment output
example_pathfindR_output_clustered for the RA example pathfindR clustering output
example_experiment_matrix for the RA differentially-expressed genes expression matrix
run_pathfindR for details on the pathfindR enrichment analysis