Find the subnetwork of significant edges n / 2 hops away from each gene.

Find the subnetwork of significant edges n / 2 hops away from each gene.

Usage

FindSignificantEdgesForHop(
  geneSet,
  combinedNetwork,
  hopConstraint,
  pValues,
  verbose = FALSE,
  topX = NULL
)

Arguments

geneSet

A character vector of genes comprising the targets of interest.

combinedNetwork

A concatenation of n PANDA-like networks with the following format: tf,gene,score_net1, score_net2, ... , score_netn

hopConstraint

The maximum number of hops to be considered for a gene.

pValues

The p-values for all edges.

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.