kda.start: Import data for weighted key driver analysis

In Mergeomics: Integrative network analysis of omics data

Description

kda.start converts identities (such as module descriptions, module identifiers, and module nodes) to indices. It prepares graph topology and module information for wKDA process.

Usage

kda.start(job)

Arguments

job	a data frame including fields for edges and nodes information of the graph (TAIL, HEAD, WEIGHT). It also involves path of input files including module descriptions and module-gene lists.

Details

kda.start imports graph and relevant module descriptor input files, creates an indexed graph structure, and converts identities to indices from module descriptions and module-gene lists. Hence, it concludes with a graph structure and a module set involving member gene IDs for each module.

Value

job	Updated data frame including indexed graph topology, modules, and nodes information: graph: indexed topology modules: module identities modinfo: module descriptions (indexed) moddata: module data (indexed) module2nodes: lists of node indices for each module modulesizes: module sizes

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, kda.prepare, kda.start.edges, kda.start.identify, kda.start.modules

Examples

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

## kda.start() process takes long time while seeking hubs in the given net
## Here, we used a very small subset of the module list (1st 10 mods
## from the original module file):
moddata <- tool.read(job.kda$modfile)
mod.names <- unique(moddata$MODULE)[1:min(length(unique(moddata$MODULE)),
10)]
moddata <- moddata[which(!is.na(match(moddata$MODULE, mod.names))),]
## save this to a temporary file and set its path as new job.kda$modfile:
tool.save(moddata, "subsetof.supersets.txt")
job.kda$modfile <- "subsetof.supersets.txt"

job.kda <- kda.configure(job.kda)
## Import data for weighted key driver analysis:
job.kda <- kda.start(job.kda) 

## Remove the temporary files used for the test:
file.remove("subsetof.supersets.txt")
## remove the results folder
unlink("Results", recursive = TRUE)

Example output

Writing to file... 
Saved 1346 rows in 'subsetof.supersets.txt'.
[1] "subsetof.supersets.txt"

KDA Version:12.7.2015

Parameters:
  Search depth: 1
  Search direction: 1
  Maximum overlap: 0.33
  Minimum module size: 20
  Minimum degree: automatic
  Maximum degree: automatic
  Edge factor: 0
  Random seed: 1

Importing edges...
     TAIL               HEAD               WEIGHT 
 Length:140663      Length:140663      Min.   :1  
 Class :character   Class :character   1st Qu.:1  
 Mode  :character   Mode  :character   Median :1  
                                       Mean   :1  
                                       3rd Qu.:1  
                                       Max.   :1  

Importing modules...
    MODULE              NODE          
 Length:825         Length:825        
 Class :character   Class :character  
 Mode  :character   Mode  :character  
Graph: 7.251717 Mb
[1] TRUE

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