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

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

diff --git a/EBSeq/man/QQP.Rd b/EBSeq/man/QQP.Rd
deleted file mode 100644 (file)
index 6fdde4e..0000000
--- a/EBSeq/man/QQP.Rd
+++ /dev/null
@@ -1,81 +0,0 @@
-\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