Perform Enrichment Analyses on the Input Subnetworks

enrichment_analyses(
  snws,
  sig_genes_vec,
  pin_name_path = "Biogrid",
  genes_by_term = pathfindR.data::kegg_genes,
  term_descriptions = pathfindR.data::kegg_descriptions,
  adj_method = "bonferroni",
  enrichment_threshold = 0.05,
  list_active_snw_genes = FALSE
)

Arguments

snws

a list of subnetwork genes (i.e., vectors of genes for each subnetwork)

sig_genes_vec

vector of significant gene symbols. In the scope of this package, these are the input genes that were used for active subnetwork search

pin_name_path

Name of the chosen PIN or path/to/PIN.sif. If PIN name, must be one of c("Biogrid", "STRING", "GeneMania", "IntAct", "KEGG", "mmu_STRING"). If path/to/PIN.sif, the file must comply with the PIN specifications. (Default = "Biogrid")

genes_by_term

List that contains genes for each gene set. Names of this list are gene set IDs (default = kegg_genes)

term_descriptions

Vector that contains term descriptions for the gene sets. Names of this vector are gene set IDs (default = kegg_descriptions)

adj_method

correction method to be used for adjusting p-values. (default = "bonferroni")

enrichment_threshold

adjusted-p value threshold used when filtering enrichment results (default = 0.05)

list_active_snw_genes

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

Value

a dataframe of combined enrichment results. Columns are:

ID

ID of the enriched term

Term_Description

Description of the enriched term

Fold_Enrichment

Fold enrichment value for the enriched term

p_value

p value of enrichment

adj_p

adjusted p value of enrichment

support

the support (proportion of active subnetworks leading to enrichment over all subnetworks) for the gene set

non_Signif_Snw_Genes (OPTIONAL)

the non-significant active subnetwork genes, comma-separated

See also

enrichment for the enrichment analysis for a single gene set

Examples

enr_res <- enrichment_analyses(snws = example_active_snws[1:2],
                               sig_genes_vec = RA_input$Gene.symbol[1:25],
                               pin_name_path = "KEGG")