cAMARETTO_ModuleNetwork: cAMARETTO_ModuleNetwork Creates a module network.

In broadinstitute/ImagingAMARETTO: ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

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
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

cAMARETTOnetworkM<-cAMARETTO_ModuleNetwork(cAMARETTOresults,0.10,5)

broadinstitute/ImagingAMARETTO documentation built on Dec. 3, 2019, 6:38 p.m.