kda2cytoscape.edges: Find edges of a given node with a specified depth

Description

kda2cytoscape.edges finds the sub-graph (node and edge lists) of a central node and its neighborhood at a particular search depth. The central node is a member of a module, which is defined at kda2cytoscape.exec.

Usage

kda2cytoscape.edges(graph, center, depth, direction)

Arguments

graph

entire graph

center

the node, whose interactions with neighbors will be searched within graph.

depth

search depth for graph neighborhood

direction

edge direction. 0 for undirected, negative for downstream and positive for upstream

Value

g: the sub-graph including TAIL, HEAD, WEIGHT information of the central node, which belongs to the specified module.

References

Shu L, Zhao Y, Kurt Z, Byars S, Tukiainen T, Kettunen J, Ripatti S, Zhang B, Inouye M, Makinen VP, Yang X. Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems. bioRxiv doi: http://dx.doi.org/10.1101/036012

Examples

Run this code

## get the prepared and KDA applied dataset:(see kda.analyze for details)
data(job_kda_analyze)
## set the relevant parameters:
job.kda$label<-"HDLC"
## parent folder for results
job.kda$folder<-"Results"
## Input a network
## columns: TAIL HEAD WEIGHT
job.kda$netfile<-system.file("extdata","network.mouseliver.mouse.txt", 
package="Mergeomics")
## Gene sets derived from ModuleMerge, containing two columns, MODULE, 
## NODE, delimited by tab 
job.kda$modfile<- system.file("extdata","mergedModules.txt", 
package="Mergeomics")
## "0" means we do not consider edge weights while 1 is opposite.
job.kda$edgefactor<-0.0
## The searching depth for the KDA
job.kda$depth<-1
## 0 means we do not consider the directions of the regulatory interactions
## while 1 is opposite.
job.kda$direction <- 1

## Finish the KDA process
job.kda <- kda.finish(job.kda)
## Select a center node to seek its neighbors in the graph:
edges.of.center.node <- kda2cytoscape.edges(job.kda$graph, 1, 
job.kda$depth, job.kda$direction)

## remove the results folder
unlink("Results", recursive = TRUE)