kda.finish.estimate {Mergeomics} | R Documentation

## Estimate measures for accomplished wKDA results

### Description

Estimates additional measures based on overlapping of module member nodes with hub neighbor nodes in the graph.

### Usage

    kda.finish.estimate(job)

### Arguments

`job` | The data list that was subjected to wKDA. It involves the modules, member genes belonging to each module, graph information of the dataset, hubs and hubnets of the graph.

### Details

`kda.finish.save` determines the overlaps of modules with hub neighborhoods, obtains graph measures based on the ratio of the observed overlap amounts to the expected overlap amount, and returns the values of this measure.

### Value

`res` | Returns the overlapping ratio of the modules with hubnets.

### 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.save`, `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)
    # }

[Package Mergeomics version 1.20.0 Index]