example_comparison_output: Second Example Output for the pathfindR Enrichment Workflow...

In pathfindR.data: Data Package for 'pathfindR'

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

pathfindR.data documentation built on May 29, 2024, 3:09 a.m.