Mergeomics (version 1.0.0)

kda.finish.save: 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.

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.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)
# }