kda2cytoscape.edges {Mergeomics} | R Documentation

## 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.

### 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)

[Package Mergeomics version 1.15.0 Index]