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

In Mergeomics: Integrative network analysis of omics data

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.

Author(s)

Zeyneb Kurt

References

Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen V-P, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC genomics. 2016;17(1):874.

See Also

kda2cytoscape

Examples

## 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)

Example output

Finishing results...

Writing to file... 
Saved 374 rows in 'Results/kda/HDLC.hubs.txt'.

Writing to file... 
Saved 446 rows in 'Results/kda/HDLC.results.txt'.

Writing to file... 
Saved 446 rows in 'Results/kda/HDLC.pvalues.txt'.

Writing to file... 
Saved 12 rows in 'Results/kda/HDLC.tophits.txt'.

Mergeomics documentation built on Nov. 8, 2020, 6:58 p.m.