Included EBSeq for downstream differential expression analysis

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

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+\name{TopCts}
+\alias{TopCts}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+Get FDR of Top Counts 
+}
+\description{
+
+}
+\usage{
+TopCts(pvalue, PP = NULL, TrueNames, TopNum)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{pvalue}{
+A matrix contains the p values (Posterior probabilities) for each transcript and each method.
+Rows are for different methods and columns are for different transcripts.
+}
+  \item{PP}{
+The length of PP vector should be the same as the number of columns in pvalue matrix.
+The value in PP either 0 or 1.
+If the ith value of PP is 0, it means the ith method (the ith row of pvalue) provided p-values.
+If the ith value of PP is 1, it means the ith method (the ith row of pvalue) provided posterior probabilities. 
+}
+  \item{TrueNames}{
+The names of the transcripts who defined to be DE.
+}
+  \item{TopNum}{
+The number of top counts we are interested in.
+For example, if TopNum=1000, we'll calculate the FDR's of each method if we pick the top 1, 2, ... 1000 genes.
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+A metrix contains the FDR's.
+}
+\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(pvalue, PP=NULL, TrueNames, TopNum){
+       NumOfMethods=ncol(pvalue)
+       puse=pvalue
+       if(1\%in\%PP)puse[,PP==1]=1-pvalue[,PP==1]
+       #puse.list=data.frame(puse)
+       FD=matrix(rep(0,NumOfMethods*TopNum),ncol=NumOfMethods)
+#      Rank=apply(puse,2,rank)
+#      for(i in 1:TopNum)
+#              FD[i,]=sapply(1:NumOfMethods, function(j)sum(!rownames(Rank)[Rank[,j]<=i]\%in\%TrueNames))      
+#      FD=sapply(1:TopNum, function(i)sapply(1:NumOfMethods, function(j)sum(!rownames(Rank)[Rank[,j]<=i]\%in\%TrueNames)))
+       for (s in 1:NumOfMethods){
+               tmp=puse[,s]
+               names(tmp)=rownames(puse)
+               sorttmp=sort(tmp)
+               for( c in 2:TopNum)
+                       FD[c, s]=FD[(c-1),s]+as.numeric(!names(sorttmp)[c]\%in\%TrueNames)
+       }
+       FD
+       #matplot(TopNum,FD,type="l",ylim=c(0,1),xlab="Top DE selected", ylab="FDR")
+       #legend("rightbottom",col=1:TopNum, lty=1:TopNum, names)
+       }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line