| kda.finish {Mergeomics} | R Documentation |
After wKDA process is accomplished, kda.finish.estimate sums
up the results and log them to the relevant files and folders. Besides,
return them within the given job parameter.
kda.finish(job)
job |
the data list including label and folder fields to specify a unique identifier for the wKDA process and the output folder for the obtained results, respectively. |
kda.finish.estimate estimates additional measures if needed,
saves results into relevant files, trims numbers to provide a simpler file
for viewing, and stores a summary file of top hits after the wKDA prcess is
accomplished. It also obtains the overlaps of the modules with hub
neighborhoods, finds co-hubs information, determines the top key driver
for each module and saves the updated and sorted p-values belonging to
them.
job |
updated information including the overlapping hub neighborhoods, co-hubs information, top driver of each module, and their updated and sorted p-values. |
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.finish.estimate, kda.finish.save,
kda.finish.summarize, kda.finish.trim
## 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)
## remove the results folder
unlink("Results", recursive = TRUE)