kda.finish.summarize: Summarize the wKDA results

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

View source: R/cle.LS.R

Description

Create a summary file of top key drivers. The file includes the key driver of each block of the dataset and their p-values.

Usage

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Arguments

res

the data frame including the p-values, false discovery rates, and fold scores of the nodes obtained from kda.finish.trim

job

the data frame including the path of output file which will briefly contain top key drivers of the blocks and ranked p-values of those top key drivers

Details

kda.finish.summarize determines the ranking scores of blocks, finds the top node for each block, selects and saves top key drivers, and stores P-values into file. top drovers of the blocks are also returned to the user.

Value

res

data frame including top node for each block

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.save, 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)
##  Create a simpler file for viewing by trimming floating numbers
#   res <- kda.finish.trim(res, job.kda)
##  Create a summary file of top hit KDs.
#   res <- kda.finish.summarize(res, job.kda)
# }
## See kda.analyze() and kda.finish() for details

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