Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/man/GetNg.Rd b/EBSeq/man/GetNg.Rd
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+\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 }