SignificantBreadthFirstSearch: Find all significant edges adjacent to the starting nodes,...

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Find all significant edges adjacent to the starting nodes, excluding the nodes specified.

Description

Find all significant edges adjacent to the starting nodes, excluding the nodes specified.

Usage

SignificantBreadthFirstSearch(
  networks,
  pValues,
  startingNodes,
  nodesToExclude,
  startFromTF,
  verbose = FALSE,
  topX = NULL
)

Arguments

networks	A concatenation of n PANDA-like networks with the following format: tf,gene,score_net1, score_net2, ... , score_netn Edges must be specified as "tf__gene".
pValues	The p-values from the original network.
startingNodes	The list of nodes from which to start.
nodesToExclude	The list of nodes to exclude from the search.
startFromTF	Whether to start from transcription factors (TRUE) or genes (FALSE).
verbose	Whether or not to print detailed information about the run.
topX	Select the X lowest significant p-values for each gene. NULL by default.

Value

A bipartite subnetwork in the same format as the original networks.

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.