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

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

diff --git a/EBSeq/man/TPFDRplot.Rd b/EBSeq/man/TPFDRplot.Rd
deleted file mode 100644 (file)
index 15e1caa..0000000
--- a/EBSeq/man/TPFDRplot.Rd
+++ /dev/null
@@ -1,103 +0,0 @@
-\name{TPFDRplot}
-\alias{TPFDRplot}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{
-Plot the number of top counts vs FDR for each method in simulation data
-}
-\description{
-%%  ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-TPFDRplot(DESeqP, EBZ, TrueDE, main, FDR = NULL)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
-  \item{DESeqP}{
-%%     ~~Describe \code{DESeqP} here~~
-}
-  \item{EBZ}{
-%%     ~~Describe \code{EBZ} here~~
-}
-  \item{TrueDE}{
-%%     ~~Describe \code{TrueDE} here~~
-}
-  \item{main}{
-%%     ~~Describe \code{main} here~~
-}
-  \item{FDR}{
-%%     ~~Describe \code{FDR} here~~
-}
-}
-\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{
-%%  ~~who you are~~
-}
-\note{
-%%  ~~further notes~~
-}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-}
-\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==>  Define data, use random,
-##--   or do  help(data=index)  for the standard data sets.
-
-## The function is currently defined as
-function(DESeqP, EBZ, TrueDE, main, FDR=NULL){
-       Seq=seq(0.001,0.5,by=0.001)
-       DETPR=rep(0,length(Seq))
-       EBTPR=rep(0,length(Seq))
-       DEFDR=rep(0,length(Seq))
-       EBFDR=rep(0,length(Seq))
-       DETPNum=rep(0,length(Seq))
-    EBTPNum=rep(0,length(Seq))
-    DEFDNum=rep(0,length(Seq))
-    EBFDNum=rep(0,length(Seq))
-       for (i in 1:length(Seq)){
-               DESeqOnes=names(DESeqP)[DESeqP<=Seq[i]]
-               if (length(FDR)==0) EBOnes=names(EBZ)[EBZ>=crit.fun(1-EBZ, Seq[i])]
-               else if (FDR=="H") EBOnes=names(EBZ)[EBZ>=(1-Seq[i])]
-                       else EBOnes=names(EBZ)[EBZ>=FDR[i]]
-
-               DETPNum[i]=sum(DESeqOnes\%in\%TrueDE)
-               EBTPNum[i]=sum(EBOnes\%in\%TrueDE)
-               DEFDNum[i]=sum(!DESeqOnes\%in\%TrueDE)
-               EBFDNum[i]=sum(!EBOnes\%in\%TrueDE)
-               
-               DETPR[i]=DETPNum[i]/length(TrueDE)
-               EBTPR[i]=EBTPNum[i]/length(TrueDE)
-               DEFDR[i]=DEFDNum[i]/length(TrueDE)
-               EBFDR[i]=EBFDNum[i]/length(TrueDE)
-       }
-       plot(Seq,DETPR,ylim=c(0,1),xlim=c(0,.5),type="l",col="red", main=paste(main, "TPR"),xlab="controled FDR level", ylab="TPR",lwd=2)
-       lines(Seq,EBTPR,col="blue",lwd=2)
-       legend("bottomright",lwd=2, col=c("red","blue"), c("DESeq","EBSeq"))
-
-       plot(Seq,DEFDR,ylim=c(0,1),xlim=c(0,.5),type="l",col="red", main=paste(main, "FDR"),xlab="controled FDR level", ylab="TPR",lwd=2)
-       lines(Seq,EBFDR,col="blue",lwd=2)
-       legend("topleft", lwd=2, col=c("red","blue"), c("DESeq","EBSeq"))
-
-
-       output=cbind( DETPR,EBTPR, DEFDR,EBFDR,DETPNum,EBTPNum,DEFDNum,EBFDNum)
-  }
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line