changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

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

diff --git a/EBSeq/man/MergeGene.Rd b/EBSeq/man/MergeGene.Rd
deleted file mode 100644 (file)
index 77044c3..0000000
--- a/EBSeq/man/MergeGene.Rd
+++ /dev/null
@@ -1,61 +0,0 @@
-\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