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

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

diff --git a/EBSeq/man/TopCts.Rd b/EBSeq/man/TopCts.Rd
deleted file mode 100644 (file)
index bf57d8d..0000000
--- a/EBSeq/man/TopCts.Rd
+++ /dev/null
@@ -1,85 +0,0 @@
-\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