pathfindR (version 1.3.0)

enrichment_analyses: Perform Enrichment Analyses on the Input Subnetworks

Description

Perform Enrichment Analyses on the Input Subnetworks

Usage

enrichment_analyses(snws, input_genes, gene_sets = "KEGG",
  custom_genes = NULL, custom_pathways = NULL, pin_path,
  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)

input_genes

vector of input gene symbols (that were used during active subnetwork genes)

gene_sets

the gene sets used for enrichment analysis. Available gene sets are KEGG, Reactome, BioCarta, GO-All, GO-BP, GO-CC, GO-MF or Custom. If "Custom", the arguments custom_genes and custom pathways must be specified. (Default = "KEGG")

custom_genes

a list containing the genes involved in each custom pathway. Each element is a vector of gene symbols located in the given pathway. Names correspond to the ID of the pathway.

custom_pathways

A list containing the descriptions for each custom pathway. Names of the list correspond to the ID of the pathway.

pin_path

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

adj_method

correction method to be used for adjusting p-values of pathway enrichment results (Default: 'bonferroni', see ?p.adjust)

enrichment_threshold

threshold used when filtering individual iterations' pathway enrichment results

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 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

See Also

enrichment for the enrichment analysis for a single gene set

Examples

# NOT RUN {
enr_res <- enrichment_analyses(snws, input_genes = my_input$GENE,
gene_sets = "KEGG", pin_path = "path/to/PIN")
# }
# NOT RUN {
# }