Included EBSeq for downstream differential expression analysis

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

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