filterActiveSnws: 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

filterActiveSnws(
  active_snw_path,
  sig_genes_vec,
  score_quan_thr = 0.8,
  sig_gene_thr = 0.02
)

Arguments

active_snw_path	path to the output of an Active Subnetwork Search
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

path2snw_list <- system.file(
  'extdata/resultActiveSubnetworkSearch.txt',
  package = 'pathfindR'
)
filtered <- filterActiveSnws(
  active_snw_path = path2snw_list,
  sig_genes_vec = example_pathfindR_input$Gene.symbol
)

pathfindR documentation built on Oct. 9, 2023, 1:07 a.m.