pathfindR (version 1.2.3)

parseActiveSnwSearch: Parse Active Subnetwork Search Output File

Description

Parse Active Subnetwork Search Output File

Usage

parseActiveSnwSearch(active_snw_path, signif_genes, score_quan_thr = 0.8,
  sig_gene_thr = 10)

Arguments

active_snw_path

path to the output of an Active Subnetwork Search.

signif_genes

the vector of significant genes.

score_quan_thr

active subnetwork score quantile threshold (Default = 0.80)

sig_gene_thr

threshold for minimum number of significant genes (Default = 10)

Value

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

See Also

See run_pathfindR for the wrapper function of the pathfindR workflow

Examples

# NOT RUN {
parseActiveSnwSearch("path/to/output", significant_genes)
# }