RA_comparison_output: Second Example Output for the pathfindR Enrichment Workflow

Description Usage Format See Also

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 Oct 19, 2020.

Usage

1

Format

A data frame with 35 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

RA_input for the RA differentially-expressed genes data frame RA_output for the RA example pathfindR enrichment output 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


pathfindR.data documentation built on Nov. 20, 2020, 5:08 p.m.