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

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

diff --git a/EBSeq/man/GetData.Rd b/EBSeq/man/GetData.Rd
deleted file mode 100644 (file)
index fbd977f..0000000
--- a/EBSeq/man/GetData.Rd
+++ /dev/null
@@ -1,94 +0,0 @@
-\name{GetData}
-\alias{GetData}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{
-Read in RSEM output of Gould data
-}
-\description{
-%%  ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-GetData(path, Name1, Name2, type)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
-  \item{path}{
-The path of RSEM outputs
-}
-  \item{Name1}{
-The output names of the files from Condition 1
-}
-  \item{Name2}{
-The output names of the files from Condition 2
-}
-  \item{type}{
-If type="G", read in the gene level output
-If type="I", read in the isoform level output
-}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-}
-\value{
-The output is the "nu values" from RSEM.
-To generate a expression matrix, the user need to run the PoolMatrix function.
-}
-\references{
-%% ~put references to the literature/web site here ~
-}
-\author{
-Ning Leng
-}
-\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(path,Name1,Name2,type)
-{
-Data=vector("list",8)
-Filenames=NULL
-Tablenames=NULL
-for (name in 1:4)
-       {
-               if (type=="I")
-                       Filenames=c(Filenames,paste(path,Name1,name,"_isoform_nus.tab",sep=""))  
-               if (type=="G")  
-                       Filenames=c(Filenames,paste(path,Name1,name,"_gene_nus.tab",sep=""))  
-               Tablenames=c(Tablenames,paste(Name1,name,sep=""))
-       }
-for (name in 1:4)
-       {
-               if (type=="I")
-                       Filenames=c(Filenames,paste(path,Name2,name,"_isoform_nus.tab",sep=""))
-               if (type=="G")
-                       Filenames=c(Filenames,paste(path,Name2,name,"_gene_nus.tab",sep=""))
-               Tablenames=c(Tablenames,paste(Name2,name,sep=""))
-       }
-
-
-names(Data)=Tablenames
-for (file in 1:8)
-       {
-               temp=read.table(Filenames[file],header=T)
-               temp2=as.matrix(temp[-1])
-               rownames(temp2)=as.vector(as.matrix(temp[1]))
-               Data[[file]]=temp2
-       }
-       Data
-  }
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line