Included EBSeq for downstream differential expression analysis

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

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+\name{QQP}
+\alias{QQP}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+The QQ Plot of empirical q's and simulated q's from fitted beta distribution
+}
+\description{
+
+}
+\usage{
+QQP(QList, AlphaResult, BetaResult, 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. 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 BetaResult.
+
+}
+  \item{AlphaResult}{
+The fitted parameter alpha from the output of NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi. Input should be a number if AList is not defined.
+}
+  \item{BetaResult}{
+The fitted parameter beta from the output of NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi. 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{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+Ning Leng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+ NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi , DenNHist
+}
+\examples{
+GeneData=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")
+
+EBres=NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi(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)), maxround=5)
+
+QQP(QList=EBres$QList1, AlphaResult=EBres[[1]][5,1], BetaResult=EBres[[2]][5,1], name="Gene", AList="F", GroupName=NULL)
+
+## The function is currently defined as
+function(QList,AlphaResult,BetaResult,name,AList="F",GroupName){
+                   for (i in 1:length(BetaResult)){
+                               tmpSize=length(QList[[i]][QList[[i]]<1])
+                       if (AList=="F") rdpts=rbeta(tmpSize,AlphaResult,BetaResult[i])
+                               else rdpts=rbeta(tmpSize,AlphaResult[i],BetaResult[i])
+       qqplot(QList[[i]][QList[[i]]<1], rdpts, xlab="estimated q's", "simulated q's from fitted beta distribution",main=paste(names(name,GroupName[i],sep=" "),xlim=c(0,1),ylim=c(0,1))
+                       }
+  }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line