kda.start.edges {Mergeomics} | R Documentation

## Import nodes and edges of graph topology

### Description

`kda.start.edges` imports network file, gets edge data (in TAIL, HEAD, WEIGHT format), eliminates the nodes -whose degree is smaller than the maximum allowed node degree-, and returns the edges of remaining nodes.

### Usage

    kda.start.edges(job)

### Arguments

`job` | a data frame including information such as network file name, maximum allowed node degree, edge direction (`job$netfile`, `job$maxdegree`, `job$direction`, and so on.)

### Value

`edgdata` | filtered edge list, i.e. edges of the nodes, whose degree is smaller than the maximum allowed node degree

### Author(s)

Ville-Petteri Makinen

### 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

`kda.analyze`, `kda.finish`, `kda.prepare`, `kda.start`

### Examples

    job.kda <- list()
    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$direction <- 1
    job.kda$nperm <- 20 # the default value is 2000, use 20 for unit tests
    job.kda <- kda.configure(job.kda)

    ## Import topology of the graph for KDA
    ## This is already had been done in the kda.start() main function, due to
    ## the time constraint while running examples, we did not run it again.
    # edgdata <- kda.start.edges(job.kda)

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

[Package Mergeomics version 1.12.0 Index]