pathfindR (version 1.4.2)

filterActiveSnws: 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 (Default = 0.80) Must be between 0 and 1 or set to -1 for not filtering

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 of genes in every active subnetwork that has a score greater than the `score_quan_thr`th quantile and that contains at least `sig_gene_thr` of significant genes.

See Also

See run_pathfindR for the wrapper function of the pathfindR enrichment workflow

Examples

# NOT RUN {
path2snw_list <- system.file("extdata/resultActiveSubnetworkSearch.txt",
                              package = "pathfindR")
filtered <- filterActiveSnws(active_snw_path = path2snw_list,
                             sig_genes_vec = pathfindR::RA_input$Gene.symbol)
unlink("active_snw_search", recursive = TRUE)
# }