kda.start.edges: Import nodes and edges of graph topology

In Mergeomics: Integrative network analysis of omics data

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)

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