kda.finish.save {Mergeomics} | R Documentation

## Save full wKDA results

### Description

`kda.finish.save` sorts (according to KD p-values) and saves the wKDA results into specified files and folders.

### Usage

    kda.finish.save(res, job)

### Arguments

`res` | the results obtained from `kda.finish.estimate`. They will be stored into specified folder.
`job` | information including the entire graph, nodes, modules, co-hubs, top key driver of each module, and their updated and sorted p-values. All the information included `job` will be stored into relevant files.

### Value

`res` | the results obtained from `kda.finish.estimate` are merged with the module and graph nodes information gained from `job` data frame. At the end, merged information is both written to file and returned to the user.

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

### Examples

    ## get the prepared and KDA applied dataset:(see kda.analyze for details)
    data(job_kda_analyze)
    ## finish the KDA process by estimating additional measures for the modules
    ## such as module sizes, overlaps with hub neighborhoods, etc.
    # job.kda <- kda.finish(job.kda)
    # if (nrow(job.kda$results)==0){
    # cat("No Key Driver Found!!!!")
    # } else{
    ##  Estimate additional measures - see kda.analyze and kda.finish for details
    #   res <- kda.finish.estimate(job.kda)
    ##  Save full results about modules such as co-hub, nodes, P-values info etc.
    #   res <- kda.finish.save(res, job.kda)
    # }

[Package Mergeomics version 1.18.0 Index]