Parse Active Subnetwork Search Output File and Filter the Subnetworks

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 = RA_input$Gene.symbol)