ESEA (version 1.0)

SavePathway2File: Save a pathway-result network to a file which can be input to the Cytoscape software

Description

Save a pathway-result network to a file which can be input to the Cytoscape software.

Usage

SavePathway2File(network, layout = layout.random, name = "network", file = "Graph")

Arguments

network

A dataframe of pathway-result network obtained from the ESEA.main function

layout

A matrix of x-y coordinates with two dims. Determine the placement of the nodes for drawing a graph.The default is "layout.random".

name

The required variables for XGMML.destription. The default is "network"

file

A character string for file name. The default is "Graph"

Examples

## Not run: 
# 
# #get example data
# dataset<-GetExampleData("dataset")
# class.labels<-GetExampleData("class.labels")
# controlcharactor<-GetExampleData("controlcharactor")
# 
# #get the data for background set of edges
# edgesbackgrand<-GetEdgesBackgrandData()
# 
# #get the edge sets of pathways
# pathwayEdge.db<-GetPathwayEdgeData()
# 
# #calculate the differential correlation score for edges
# EdgeCorScore<-calEdgeCorScore(dataset, class.labels, controlcharactor,edgesbackgrand)
# 
# #identify dysregulated pathways by using the function ESEA.Main
# #Results<-ESEA.Main(EdgeCorScore,pathwayEdge.db)
# Results<-GetExampleData("PathwayResult")
# 
# #obtain the detail results of genes for a significant pathway
# PathwayNetwork<-Results[[2]][[1]]
# 
# #save the pathway-result network to a file which can be input to the Cytoscape software. 
# SavePathway2File(PathwayNetwork,layout=layout.circle,file="Graph")
#   			
# ## End(Not run)