File: kda.finish.trim.Rd

package info (click to toggle)
r-bioc-mergeomics 1.34.0-2
  • links: PTS, VCS
  • area: main
  • in suites: sid, trixie
  • size: 9,200 kB
  • sloc: makefile: 4
file content (58 lines) | stat: -rw-r--r-- 1,893 bytes parent folder | download | duplicates (4)
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}}
}