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

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

diff --git a/EBSeq/man/PoolMatrix.Rd b/EBSeq/man/PoolMatrix.Rd
deleted file mode 100644 (file)
index b2c46d5..0000000
--- a/EBSeq/man/PoolMatrix.Rd
+++ /dev/null
@@ -1,82 +0,0 @@
-\name{PoolMatrix}
-\alias{PoolMatrix}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{
-Generate the expression matrix from the output of GetData
-}
-\description{
-%%  ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-PoolMatrix(Data, reads, type)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
-  \item{Data}{
-The output from GetData function.
-}
-  \item{reads}{
-The total number of reads in each lane. Could be obtained from the RSEM outputs. 
-}
-  \item{type}{
-If type="S", the outputs will be the a matrix which transcript names in row and sample names in column.
-If type="G", the first column will be the group information. 
-
-}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-}
-\value{
-\item{PoolM}{The matrix of nu values}
-\item{PoolValue}{The matrix of expression values}
-}
-\references{
-%% ~put references to the literature/web site here ~
-}
-\author{
-Ning Leng
-}
-\note{
-%%  ~~further notes~~
-}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-GetData
-}
-\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(Data,reads,type)
-{
-poolnames=names(Data)
-poolM=NULL
-for (po in 1:8)
-       poolM=cbind(poolM,Data[[po]][,1])
-rownames(poolM)=rownames(Data[[1]])
-colnames(poolM)=poolnames
-
-#poolValue=poolM*reads
-poolValue=poolM
-for (col in 1:8)
-       poolValue[,col]=poolM[,col]*reads[col]
-poolValue=round(poolValue)
-if (type=="G")
-       {
-               poolM=cbind(Data[[1]][,2],poolM)
-               poolValue=cbind(Data[[1]][,2],poolValue)
-               colnames(poolM)=c("Groups",poolnames)
-               colnames(poolValue)=c("Groups",poolnames)
-       }
-poolOutput=list(poolM=poolM,poolValue=poolValue)
-  }
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line