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

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

diff --git a/EBSeq/man/QuantileNorm.Rd b/EBSeq/man/QuantileNorm.Rd
deleted file mode 100644 (file)
index 5d9ec77..0000000
--- a/EBSeq/man/QuantileNorm.Rd
+++ /dev/null
@@ -1,54 +0,0 @@
-\name{QuantileNorm}
-\alias{QuantileNorm}
-\title{
-Quantile Normalization
-}
-\description{
-The Quantile normalization
-}
-\usage{
-QuantileNorm(Data, Quantile)
-}
-\arguments{
-
-  \item{Data}{
-The data matrix with transcripts in rows and lanes in columns.
-}
-\item{Quantile}{
-The quantile the user wishs to use. Should be a number between 0 and 1.        
-}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-Use a quantile point to normalize the data.
-}
-\value{
-The function will return a vector contains the normalization factor for each lane.
-% ...
-}
-\references{}
-\author{
-Ning Leng
-}
-\note{
-%%  ~~further notes~~
-}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-}
-\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="Y")
-GeneData=GeneGenerate$data
-
-Sizes=QuantileNorm(GeneData)
-# Run EBSeq
-EBres=EBTest(Data=GeneData, NgVector=rep(1,10^4), Vect5End=rep(1,10^4), Vect3End=rep(1,10^4), Conditions=as.factor(rep(c(1,2),each=5)), sizeFactors=Sizes,maxround=5)
-
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line