SavePathway2File: Save a pathway-result network to a file which can be input to...

In hanjunwei-lab/ESEA: ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

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 <[e-mail]>, Xinrui Shi<[e-mail]> and Chunquan Li <[e-mail]>

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)

hanjunwei-lab/ESEA documentation built on July 5, 2020, 11:01 a.m.