kda2himmeli: Generate input files for Himmeli

In zeynebkurtUCLA/Mergeomics: Integrative network analysis of omics data

Description

kda2himmeli generates input files for Himmeli to visualize the graph and hubnets after the wKDA process finished. The network visualization is a streamlined depiction of the module enrichment in hub neighborhoods.

Usage

kda2himmeli(job, modules = NULL, ndrivers = 5)

Arguments

job	KDA result data list as returned by kda.finish
modules	array of module names to be visualized
ndrivers	maximum number of drivers per module

Details

kda2himmeli first, selects top scoring key drivers for each module; then, assigns a colormap to modules, processes each module separately, finds key nodes' neighborhoods, and saves the edge and node lists of the modules to the specified output folder. Besides, it returns this configuration data to the user.

Value

job	updated data list including the node and edge information of the modules converted to Himmeli format

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

kda.analyze, kda.finish

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$netfile<-system.file("extdata","network.mouseliver.mouse.txt", 
package="Mergeomics")
job.kda$nodfile <- system.file("extdata","msea2kda.nodes.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)

## prepare the cytoscape-ready files:
job.kda <- kda2himmeli(job.kda)

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

zeynebkurtUCLA/Mergeomics documentation built on May 14, 2019, 1:59 a.m.