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Last data update: 2014.03.03

R: Save a pathway-result network to a file which can be input to...

SavePathway2File

R Documentation

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"

Author(s)

Junwei Han <hanjunwei1981@163.com>, Xinrui Shi<xinrui103@163.com> and Chunquan Li <lcqbio@163.com>

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)