pathfindR (version 1.3.0)

summarize_enrichment_results: Summarize Enrichment Results

Description

Summarize Enrichment Results

Usage

summarize_enrichment_results(enrichment_res,
  list_active_snw_genes = FALSE)

Arguments

enrichment_res

a dataframe of combined enrichment results. Columns are:

ID

KEGG ID of the enriched pathway

Pathway

Description of the enriched pathway

Fold_Enrichment

Fold enrichment value for the enriched pathway

p_value

p value of enrichment

adj_p

adjusted p value of enrichment

non_DEG_Active_Snw_Genes (OPTIONAL)

the non-DEG active subnetwork genes, comma-separated

list_active_snw_genes

boolean value indicating whether or not to report the non-DEG active subnetwork genes for the active subnetwork which was enriched for the given pathway with the lowest p value (default = FALSE)

Value

a dataframe of summarized enrichment results (over multiple iterations). Columns are:

ID

KEGG ID of the enriched pathway

Pathway

Description of the enriched pathway

Fold_Enrichment

Fold enrichment value for the enriched pathway

occurrence

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

lowest_p

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

highest_p

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

non_DEG_Active_Snw_Genes (OPTIONAL)

the non-DEG active subnetwork genes, comma-separated

Examples

# NOT RUN {
summarize_enrichment_results(enrichment_res)
# }