Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/man/DenNHist.Rd b/EBSeq/man/DenNHist.Rd
new file mode 100644 (file)
index 0000000..f096153
--- /dev/null
+++ b/EBSeq/man/DenNHist.Rd
@@ -0,0 +1,107 @@
+\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