kda.finish {Mergeomics} | R Documentation

## Organize and save results

### Description

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.

### Usage

    kda.finish(job)

### Arguments

`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.

### Details

`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.

### Value

`job` | updated information including the overlapping hub neighborhoods, co-hubs information, top driver of each module, and their updated and sorted p-values.

### 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.finish.estimate`, `kda.finish.save`, `kda.finish.summarize`, `kda.finish.trim`

### 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)

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

[Package Mergeomics version 1.10.0 Index]