kda.finish.save: Save full wKDA results

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/cle.LS.R

Description

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

Usage

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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

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## 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)
# }

zeynebkurtUCLA/Mergeomics documentation built on May 14, 2019, 1:59 a.m.