kda2cytoscape.drivers: Select top key drivers for each module

In Mergeomics: Integrative network analysis of omics data

Description

kda2cytoscape.drivers finds maximally top ndriv key drivers for each module with respect to the significance level of the drivers.

Usage

kda2cytoscape.drivers(data, modules, ndriv)

Arguments

data	data frame including information of the modules (key driver list, p-values, node list, false discovery rates (fdr), and so on.)
modules	top scoring modules among KDA results
ndriv	maximum number of drivers that can be chosen for per module

Value

data	top key drivers (maximally ndriv drivers for each module) for top modules

Author(s)

Zeyneb Kurt

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

kda2cytoscape

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$netfile<-system.file("extdata","network.mouseliver.mouse.txt", 
package="Mergeomics")
## Gene sets derived from ModuleMerge, containing two columns, MODULE, 
## NODE, delimited by tab 
job.kda$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)
## Select top key drivers from each module.
## First, take module names from kda results
modules <- unique(job.kda$results$MODULE)
## Take top 2 KDs:
drivers <- kda2cytoscape.drivers(job.kda$results, modules, ndriv=2)

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

Example output

Finishing results...

Writing to file... 
Saved 374 rows in 'Results/kda/HDLC.hubs.txt'.

Writing to file... 
Saved 446 rows in 'Results/kda/HDLC.results.txt'.

Writing to file... 
Saved 446 rows in 'Results/kda/HDLC.pvalues.txt'.

Writing to file... 
Saved 12 rows in 'Results/kda/HDLC.tophits.txt'.

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