Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/man/TPFDRplot.Rd b/EBSeq/man/TPFDRplot.Rd
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+\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