kda2himmeli.edges {Mergeomics} | R Documentation |
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
.
kda2himmeli.edges(graph, center, depth, direction)
graph |
entire graph |
center |
the node, whose interactions with neighbors will be searched within
|
depth |
search depth for graph neighborhood |
direction |
edge direction. 0 for undirected, negative for downstream and positive for upstream |
g |
the sub-graph including TAIL, HEAD, WEIGHT information of the central node, which belongs to the specified module. |
Ville-Petteri Makinen
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.
## 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)