\HeaderA{sage.library}{Class sage.library}{sage.library}
\aliasA{plot.sage.library}{sage.library}{plot.sage.library}
\aliasA{print.sage.library}{sage.library}{print.sage.library}
\aliasA{read.sage.library}{sage.library}{read.sage.library}
\aliasA{summary.sage.library}{sage.library}{summary.sage.library}
\aliasA{write.sage.library}{sage.library}{write.sage.library}
\keyword{IO}{sage.library}
\begin{Description}\relax
The SAGE library class contains all the data and annotation for a SAGE
library. It can contain two data.frames.
\end{Description}
\begin{Usage}
\begin{verbatim}
read.sage.library(file)
write.sage.library(x, file=paste(x\$libname, "sage", sep="."),
                   what="complete") 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] A sage library object
\item[\code{file}] File name to read or write to
\item[\code{what}] "complete", read complete librarary tags and sequences;
"tags", read only tags and counts
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
SAGE library objects consists of one or two data.frames. The
data.frame "tags" contains all the unique tags in the library and its
counts. The data.frame "seqs" contains all the individual tag
sequences and associated quality values. \code{read.sage.library} and
\code{write.sage.library} are utility functions to read and write SAGE
libraries.
\end{Details}
\begin{Author}\relax
Tim Beissbarth
\end{Author}
\begin{References}\relax
\url{http://tagcalling.mbgproject.org}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{extract.lib}{extract.lib}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
library(sagenhaft)
E15postHFI <- read.sage.library(system.file("data/E15postHFI.sage",
                                package="sagenhaft")) 
E15postHFI
\end{ExampleCode}
\end{Examples}

