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
)a list of subnetwork genes (i.e., vectors of genes for each subnetwork)
vector of significant gene symbols. In the scope of this package, these are the input genes that were used for active subnetwork search
Name of the chosen PIN or absolute/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')
List that contains genes for each gene set. Names of this list are gene set IDs (default = kegg_genes)
Vector that contains term descriptions for the gene sets. Names of this vector are gene set IDs (default = kegg_descriptions)
correction method to be used for adjusting p-values. (default = 'bonferroni')
adjusted-p value threshold used when filtering enrichment results (default = 0.05)
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)
a dataframe of combined enrichment results. Columns are:
ID of the enriched term
Description of the enriched term
Fold enrichment value for the enriched term
p value of enrichment
adjusted p value of enrichment
the support (proportion of active subnetworks leading to enrichment over all subnetworks) for the gene set
the non-significant active subnetwork genes, comma-separated
enrichment for the enrichment analysis for a single gene set
enr_res <- enrichment_analyses(
snws = example_active_snws[1:2],
sig_genes_vec = example_pathfindR_input$Gene.symbol[1:25],
pin_name_path = 'KEGG'
)