1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58
|
\name{kda.finish.trim}
\alias{kda.finish.trim}
\title{
Trim numbers before save
}
\description{
\code{\link{kda.finish.trim}} trims p-values, false discovery rates, and
fold scores to make them nicer to look at before saving the file. It also
returns trimmed results to the user.
}
\usage{
kda.finish.trim(res, job)
}
\arguments{
\item{res}{
includes p-values, false discovery rates, and fold scores of the nodes
}
\item{job}{
data frame including output folder path to store trimmed results
}
}
\value{
\item{res }{
Trimmed and formatted p-values, false discovery rates, and fold
scores of the nodes
}
}
\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)
## Create a simpler file for viewing by trimming floating numbers
# res <- kda.finish.trim(res, job.kda)
# }
## See kda.analyze() and kda.finish() for details
}
\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.
}
\author{
Ville-Petteri Makinen
}
\seealso{
\code{\link{kda.finish}}, \code{\link{kda.finish.estimate}},
\code{\link{kda.finish.save}}, \code{\link{kda.finish.summarize}}
}
|