kda.start.modules {Mergeomics} | R Documentation |
kda.start.modules
searches the whole nodes of the modules
within the nodes of edgdata
edgelist, filters out the nodes that
does not exist in the nodes of edgdata
, and deletes the modules,
which does not have enough nodes.
kda.start.modules(job, edgdata)
job |
a data frame including information such as module data file
name, edge direction, minimum acceptable module size ( |
edgdata |
edge list data obtained from |
moddata |
module descriptions and their member node lists |
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.
kda.analyze
, kda.finish
,
kda.prepare
, kda.start
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, then find the module statistics ## 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) ## Find module memberships of the graph nodes and obtain module statistics: # moddata <- kda.start.modules(job.kda, edgdata) ## remove the results folder unlink("Results", recursive = TRUE)