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

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

diff --git a/EBSeq/man/GetNg.Rd b/EBSeq/man/GetNg.Rd
deleted file mode 100644 (file)
index 65207a4..0000000
--- a/EBSeq/man/GetNg.Rd
+++ /dev/null
@@ -1,66 +0,0 @@
-\name{GetNg}
-\alias{GetNg}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{
-Generate the Ng vector
-}
-\description{
-Generate the Ng vector for the isoforms
-}
-\usage{
-GetNg(IsoformName, GeneName)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
-  \item{IsoformName}{
-A vector contains the isoform names
-}
-  \item{GeneName}{
-The gene names of the isoforms in IsoformNames. (Should be in the same order)
-  }
-
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-}
-\value{
-  \item{GeneNg}{
-  The number of isoforms each gene contains
-  }
-  \item{GeneNgTrun}{
-  The truncated Ng of each gene. (The genes contain more than 3 isoforms are with Ng 3.)
-  }
-   \item{IsoformNg}{
-  The Ng of each isoform 
-  }
-    \item{IsoformNgTrun}{
-   The truncated Ng of each isoform. 
-  }
-
-
-}
-\references{
-}
-\author{
-Ning Leng
-}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-}
-\examples{
-IsoGenerate=IsoSimu(DVDconstant=NULL, DVDqt1=.97, DVDqt2=.98, Conditions=as.factor(rep(c(1,2),each=5)), NumofSample=10, NumofIso=c(1000,2000,3000), DEIsoProp=.1, Phiconstant=NULL, Phi.qt1=.25, Phi.qt2=.75, OnlyData=T )
-
-IsoMat=do.call(rbind,IsoGenerate$data)
-IsoNames=rownames(IsoMat)
-
-Ngvector=GetNg(IsoNames, IsosGeneNames)
-
-IsoEBres=EBTest(Data=IsoMat, NgVector=IsoNgTrun, Conditions=as.factor(rep(c(1,2),each=5)),sizeFactors=rep(1,10), maxround=5)
-
-
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ Ng }