Mergeomics (version 1.0.0)

kda.start.edges: 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

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

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)