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

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

diff --git a/EBSeq/man/DenNHist.Rd b/EBSeq/man/DenNHist.Rd
deleted file mode 100644 (file)
index f096153..0000000
--- a/EBSeq/man/DenNHist.Rd
+++ /dev/null
@@ -1,107 +0,0 @@
-\name{DenNHist}
-\alias{DenNHist}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{
-%%  ~~function to do ... ~~
-Density plot to compare th empirical q's and the simulated q's from the fitted beta distribution.
-}
-\description{
-%%  ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-DenNHist(QList, Alpha, Beta, name, AList = "F", GroupName)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
-  \item{QList}{
-The estimated q's from the output of NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar
-. Input could be a vector or a list of different groups of transcripts. The number of lists here should be the same as the length of Beta.
-
-}
-  \item{Alpha}{
-The fitted parameter alpha from the output of NBBetaEB.bias.uniqueP_PoolVarSpeed
-Up_MDFPoi_NoNormVar. Input should be a number if AList is not defined.
-}
-  \item{Beta}{
-The fitted parameter beta from the output of NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar. 
-Input could be one single number or a vector of several numbers. The length of the input should be the same as the number of lists of QList.
-
-}
-  \item{name}{
-The name of the plots
-}
-  \item{AList}{
-Whether a list of alpha's are used
-
-}
-  \item{GroupName}{
-The names of each sub plot. The l
-ength of the input should be the same as the number of lists of QList.
-
-}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-}
-\value{
-Plots will be generated. Each plot represents a sub-list of the QList.
-The empirical estimation of q's will be represented as blue histogram and the density of
-the fitted beta distribution will be represented as the green line.
-The main title of the plot will be "GroupName name".
-
-}
-\references{
-%% ~put references to the literature/web site here ~
-}
-\author{
-Ning Leng
-}
-\note{
-%%  ~~further notes~~
-}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-beta.mom, DenNHistTable, QQP, NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar
-}
-\examples{
-### Simulate Gene Level Data
-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$data
-
-# Run EBSeq
-EBres=NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar(Data=GeneData, NgVector=rep(1,10^4), Vect5End=rep(1,10^4), Vect3End=rep(1,10^4), Conditions=as.factor(rep(c(1,2),each=5)), sizeFactors=rep(1,10),maxround=5)
-# Plot
-DenNHist(QList=EBres$QList1, Alpha=EBres[[1]][5,1], Beta=EBres[[2]][5,1], name="Gene", AList="F", GroupName="")
-
-### Simulate Isoform Level Data
-IsoGenerate=IsoSimu(DVDconstant=NULL, DVDqt1=.97, DVDqt2=.98, Conditions=as.factor(rep(c(1,2),each=5)), NumofSample=10, NumofIso=NULL, DEIsoProp=.1, Phiconstant=NULL, Phi.qt1=.25, Phi.qt2=.75, OnlyData="Y" )
-IsoList=IsoGenerate$data
-
-# Get Vectors and Run EBSeq
-ngv=c(1,2,3,2,3,2,3,2,3)
-b3v=c(1,0,0,1,1,0,0,1,1)
-b5v=c(1,0,0,0,0,1,1,1,1)
-NgV=unlist(sapply(1:9,function(i)rep(ngv[i],dim(IsoList[[i]])[1])))
-Bias3V=unlist(sapply(1:9,function(i)rep(b3v[i],dim(IsoList[[i]])[1])))
-Bias5V=unlist(sapply(1:9,function(i)rep(b5v[i],dim(IsoList[[i]])[1])))
-
-IsoData=do.call(rbind,IsoList)
-IsoEBres=NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar(Data=IsoData, NgVector=NgV, Vect5End=Bias5V, Vect3End=Bias3V, Conditions=as.factor(rep(c(1,2),each=5)),sizeFactors=rep(1,10), maxround=5)
-
-# Plot
-par(mfrow=c(3,3))
-DenNHist(QList=IsoEBres$QList1, Alpha=IsoEBres[[1]][5,], Beta=IsoEBres[[2]][5,], name="Isoform", AList="F", GroupName=paste("group",c(1:9),sep=""))
-
-
-
-
-
-
-
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ beta }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line