PlotRunEnrichment: Plot running Edge enrichment score

Description Usage Arguments Author(s) Examples

View source: R/PlotRunEnrichment.R

Description

Plot running edge enrichment score for the pathway result

Usage

1
  PlotRunEnrichment(EdgeCorScore, PathwayResult, weighted.score.type = 1)

Arguments

EdgeCorScore

A numeric vector. Each element is the differential correlation score of an edge.

PathwayResult

A list of pathway result obtained from the ESEA.main function

weighted.score.type

A value. Edge enrichment correlation-based weighting: 0=no weight, 1=standard weigth, 2 = over-weigth. The default value is 1

Author(s)

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
## 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
PathwayResult<-Results[[2]][1]

#Plot running edge enrichment score for the pathway result
PlotRunEnrichment(EdgeCorScore,PathwayResult,weighted.score.type = 1)


## End(Not run)

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