XYomics (version 0.1.2)

construct_ppi_pcsf: Construct Protein-protein interaction Network using Prize-Collecting Steiner Forest

Description

Constructs a condition-specific gene regulatory network based on differential expression results using the PCSF algorithm.

Usage

construct_ppi_pcsf(
  g,
  prizes,
  w = 2,
  b = 1,
  mu = 5e-04,
  seed = 1,
  min_nodes = 1
)

Value

An igraph object representing the extracted subnetwork. Returns NULL invisibly if no prize genes are present, the subnetwork is too small, or the PCSF algorithm fails.

An igraph object representing the extracted subnetwork. Returns NULL invisibly if no prize genes are present, the subnetwork is too small, or the PCSF algorithm fails

Arguments

g

An igraph object representing the base network.

prizes

A named numeric vector of gene scores (prizes). Names must match vertex names in g.

w

Numeric. Edge cost scaling weight. Default is 2.

b

Numeric. Balance between prizes and edge costs. Default is 1.

mu

Numeric. Trade-off parameter for sparsity. Default is 5e-04.

seed

Integer. Random seed. Default is 1.

min_nodes

Integer. Minimum number of nodes in subnetwork. Default is 1.