Included EBSeq for downstream differential expression analysis

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

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+\name{DenNHistTable}
+\alias{DenNHistTable}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+9 Density plots to compare the empirical q's and the simulated q's from the fitted beta distribution.
+}
+\description{
+Check the beta fit of 9 different groups on isoform level data. 
+}
+\usage{
+DenNHistTable(QList, Alpha, Beta,  AList = "F")
+}
+%- 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 should be a list of different groups of transcripts. The number of lists here should be 9.
+
+}
+
+  \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 9.
+
+}
+
+  \item{AList}{
+Whether a list of alpha's are used
+
+}
+
+  }
+\details{
+
+}
+\value{
+A plot contains 9 dub-plots will be generated. 
+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{
+DenNHist, beta.mom, QQP, NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar
+}
+\author{
+Ning Leng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+# Generate 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$data
+
+# Get Ng Vector, 5End Vector and 3End Vector
+ngv=c(1,2,3,2,3,2,3,2,3)
+b3v=c(1,0,0,1,1,0,0,1,1)
+b5v=c(1,0,0,0,0,1,1,1,1)
+NgV=unlist(sapply(1:9,function(i)rep(ngv[i],dim(IsoList[[i]])[1])))
+Bias3V=unlist(sapply(1:9,function(i)rep(b3v[i],dim(IsoList[[i]])[1])))
+Bias5V=unlist(sapply(1:9,function(i)rep(b5v[i],dim(IsoList[[i]])[1])))
+
+#Run EBSeq
+IsoData=do.call(rbind,IsoList)
+IsoEBres=NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar(Data=IsoData, NgVector=NgV, Vect5End=Bias5V, Vect3End=Bias3V, Conditions=as.factor(rep(c(1,2),each=5)),sizeFactors=rep(1,10), maxround=5)
+
+DenNHistTable(QList=IsoEBres$QList1, Alpha=IsoEBres[[1]][5,], Beta=IsoEBres[[2]][5,], AList="F")
+
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line