filter_active_subnetworks: Parse Active Subnetwork Search Output File and Filter the...

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Parse Active Subnetwork Search Output File and Filter the Subnetworks

Description

Parse Active Subnetwork Search Output File and Filter the Subnetworks

Usage

filter_active_subnetworks(
  active_snws,
  sig_genes_vec,
  score_quan_thr = 0.8,
  sig_gene_thr = 0.02
)

Arguments

active_snws	active subnetwork search results. A list containing input subnetworks (nodes) and scores (score).
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
score_quan_thr	active subnetwork score quantile threshold. Must be between 0 and 1 or set to -1 for not filtering. (Default = 0.8)
sig_gene_thr	threshold for the minimum proportion of significant genes in the subnetwork (Default = 0.02) If the number of genes to use as threshold is calculated to be < 2 (e.g. 50 signif. genes x 0.01 = 0.5), the threshold number is set to 2

Value

A list containing subnetworks: a list of of genes in every active subnetwork that has a score greater than the score_quan_thrth quantile and that contains at least sig_gene_thr of significant genes and scores the score of each filtered active subnetwork

See Also

See run_pathfindR for the wrapper function of the pathfindR enrichment workflow

Examples

filtered <- filter_active_subnetworks(
  active_snws = example_unfiltered_snws,
  sig_genes_vec = example_pathfindR_input$Gene.symbol
)

pathfindR documentation built on July 2, 2026, 1:06 a.m.