kda2himmeli.edges: Find edges of a given node with a specified depth

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/cle.LS.R

Description

kda2himmeli.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 kda2himmeli.exec.

Usage

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kda2himmeli.edges(graph, center, depth, direction)

Arguments

graph

entire graph

center

the node, whose interactions with neighbors will be searched within graph.

depth

search depth for graph neighborhood

direction

edge direction. 0 for undirected, negative for downstream and positive for upstream

Value

g

the sub-graph including TAIL, HEAD, WEIGHT information of the central node, which belongs to the specified module.

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

kda2himmeli

Examples

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## 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")
job.kda$nodfile <- system.file("extdata","msea2kda.nodes.txt", 
package="Mergeomics")
## "0" means we do not consider edge weights while 1 is opposite.
job.kda$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 <- kda2himmeli.edges(job.kda$graph, 1, 
job.kda$depth, job.kda$direction)

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

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