Mergeomics (version 1.0.0)

kda.finish.estimate: 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.

Value

res

Returns the overlapping ratio of the modules with hubnets.

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.

References

Shu L, Zhao Y, Kurt Z, Byars S, Tukiainen T, Kettunen J, Ripatti S, Zhang B, Inouye M, Makinen VP, Yang X. Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems. bioRxiv doi: http://dx.doi.org/10.1101/036012

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)
# }