tool.graph.list: Return edge list for each node

In zeynebkurtUCLA/Mergeomics: Integrative network analysis of omics data

Description

tool.graph.list finds and returns the edge list of each node for both tail and head node lists.

Usage

tool.graph.list(entries, nnodes)

Arguments

entries	either tail nodes list or head nodes list
nnodes	total number of all nodes including both tails and heads

Value

groups

a data list including edge list of each node

Author(s)

Ville-Petteri Makinen

See Also

tool.graph

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$netfile<-system.file("extdata","network.mouseliver.mouse.txt", 
package="Mergeomics")
## module file:
job.kda$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

## kda.start() process takes long time while seeking hubs in the given net
## Here, we used a very small subset of the module list (1st 10 mods
## from the original module file):
moddata <- tool.read(job.kda$modfile)
mod.names <- unique(moddata$MODULE)[1:min(length(unique(moddata$MODULE)),
10)]
moddata <- moddata[which(!is.na(match(moddata$MODULE, mod.names))),]
## save this to a temporary file and set its path as new job.kda$modfile:
tool.save(moddata, "subsetof.supersets.txt")
job.kda$modfile <- "subsetof.supersets.txt"

job.kda <- kda.configure(job.kda)

## Import data for weighted key driver analysis:
## Import topology.
edges <- kda.start.edges(job.kda)
## Create an indexed graph structure.
tails <- as.character(edges$TAIL)
heads <- as.character(edges$HEAD)
wdata <- as.double(edges$WEIGHT)

nedges <- length(tails)
# Create factorized representation.
labels <- as.character(c(tails, heads))
labels <- as.factor(labels)
labelsT <- as.integer(labels[1:nedges])
labelsH <- as.integer(labels[(nedges+1):(2*nedges)])
# Create edge lists.
nodnames <- levels(labels)
nnodes <- length(nodnames)
elistT <- tool.graph.list(labelsT, nnodes)
elistH <- tool.graph.list(labelsH, nnodes)
## Remove the temporary files used for the test:
file.remove("subsetof.supersets.txt")

zeynebkurtUCLA/Mergeomics documentation built on May 14, 2019, 1:59 a.m.