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

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.