Included EBSeq for downstream differential expression analysis

[rsem.git] / EBSeq / man / MergeGene.Rd

diff --git a/EBSeq/man/MergeGene.Rd b/EBSeq/man/MergeGene.Rd
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+\name{MergeGene}
+\alias{MergeGene}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+Plots of gene simulation result
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+MergeGene(GeneSIMout, Num, Path = "./")
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{GeneSIMout}{
+The output of GeneSimu with OnlyData="F".
+}
+  \item{Num}{
+How many times the simulation ran.
+}
+  \item{Path}{
+The path to store the plots
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+3 plots will be generated.
+1 FPR vs TPR of each method
+2 FDR vs TPR of each method
+2 Top counts vs FDR of each method
+
+A table will be generated which contains the FDR and TPR of each method.
+(Using p-value=.05 or Posterior Probability=.95).
+
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+Ning Leng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+IsoMerge
+}
+\examples{
+GeneGenerate=GeneSimu(DVDconstant=4, DVDqt1=NULL, DVDqt2=NULL, Conditions=rep(c(1,2),each=5), NumofSample=10, NumofGene=10000, DEGeneProp=.1, Phiconstant=NULL, Phi.qt1=.25, Phi.qt2=.75, Meanconstant=NULL, OnlyData="F")
+
+GeneTable=MergeGene(GeneGenerate,1,"./")
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line