cAMARETTO_ModuleNetwork: cAMARETTO_ModuleNetwork Creates a module network.

In broadinstitute/CommunityAMARETTO: CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Description

cAMARETTO_ModuleNetwork

Creates a module network.

Usage

cAMARETTO_ModuleNetwork(
  cAMARETTOresults,
  pvalue = 0.05,
  inter = 5,
  color_list = NULL,
  edge_method = "pvalue",
  plot_network = TRUE
)

Arguments

cAMARETTOresults	cAMARETTOresults object
pvalue	pvalue cut-off for each gene set
inter	minimal overlap between two gene sets
color_list	An optional list with colors
edge_method	Define edge weights based p-values or overlap between the gene sets.
plot_network	If TRUE, plots the Community Network at the end.

Value

a list with the module network, layout for the network, used p-value, used overlap en colors

Examples

try(
cAMARETTOnetworkM<-cAMARETTO_ModuleNetwork(cAMARETTOresults,0.10,5)
)

broadinstitute/CommunityAMARETTO documentation built on April 6, 2020, 10:44 p.m.