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\name{kda2cytoscape.edges}
\alias{kda2cytoscape.edges}
\title{
Find edges of a given node with a specified depth
}
\description{
\code{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
\code{\link{kda2cytoscape.exec}}.
}
\usage{
kda2cytoscape.edges(graph, center, depth, direction)
}
\arguments{
\item{graph}{
entire graph
}
\item{center}{
the node, whose interactions with neighbors will be searched within
\code{graph}.
}
\item{depth}{
search depth for graph neighborhood
}
\item{direction}{
edge direction. 0 for undirected, negative for downstream and positive
for upstream
}
}
\value{
\item{g }{the sub-graph including TAIL, HEAD, WEIGHT information of the
central node, which belongs to the specified module.}
}
\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)
}
\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.
}
\author{
Zeyneb Kurt
}
\seealso{
\code{\link{kda2cytoscape}}
}
|
