pathfindR (version 1.3.0)

enrichment: Perform Enrichment Analysis for a Single Gene Set

Description

Perform Enrichment Analysis for a Single Gene Set

Usage

enrichment(genes_by_pathway, genes_of_interest, pathways_list,
  adj_method = "bonferroni", enrichment_threshold, pin_path, DEG_vec)

Arguments

genes_by_pathway

List that contains genes for each pathway. Names of this list are KEGG IDs.

genes_of_interest

The set of gene symbols to be used for enrichment analysis. In the scope of this package, these are genes that were identified for an active subnetwork.

pathways_list

List that contains pathway descriptions for KEGG pathway IDs. Names of this list are KEGG IDs.

adj_method

correction method to be used for adjusting p-values.

enrichment_threshold

adjusted-p value threshold used when filtering pathway enrichment results

pin_path

path to the Protein-Protein Interaction Network (PIN) file used in the analysis

DEG_vec

vector of differentially-expressed gene symbols

Value

A data frame that contains enrichment results.

See Also

p.adjust for adjustment of p values. See run_pathfindR for the wrapper function of the pathfindR workflow. hyperg_test for the details on hypergeometric distribution-based hypothesis testing.

Examples

# NOT RUN {
pin_path <- return_pin_path("KEGG")
enrichment(kegg_genes, c("PER1", "PER2", "CRY1", "CREB1"), kegg_pathways,
           "bonferroni", 0.05, pin_path, c("PER1"))
# }