\HeaderA{sage.library.comparison}{Class sage.library.comparison}{sage.library.comparison}
\aliasA{compare.lib.pair}{sage.library.comparison}{compare.lib.pair}
\aliasA{plot.sage.library.comparison}{sage.library.comparison}{plot.sage.library.comparison}
\aliasA{print.sage.library.comparison}{sage.library.comparison}{print.sage.library.comparison}
\aliasA{read.sage.library.comparison}{sage.library.comparison}{read.sage.library.comparison}
\aliasA{summary.sage.library.comparison}{sage.library.comparison}{summary.sage.library.comparison}
\aliasA{write.sage.library.comparison}{sage.library.comparison}{write.sage.library.comparison}
\keyword{IO}{sage.library.comparison}
\begin{Description}\relax
Class for storing the data of a pairwise comparison between two SAGE
libraries.
\end{Description}
\begin{Usage}
\begin{verbatim}
read.sage.library.comparison(file)
write.sage.library.comparison(x, file=paste(x$name, "sagecomp", sep="."))
compare.lib.pair(lib1, lib2) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x,lib1,lib2}] A sage library object
\item[\code{file}] File name to read or write to
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
SAGE library comparison objects consists of one data.frames. It stores
a A and an M value which are the log2 average expression and log2
ratio, respectively. It also has a column for the resulting p.values
from \code{\LinkA{sage.test}{sage.test}}.
\code{read.sage.library.comparison} and
\code{write.sage.library.comparison} are utility functions to read and
write SAGE library comparisons. \code{compare.lib.pair} can be used to
generate SAGE library comparisons.
\end{Details}
\begin{Author}\relax
Tim Beissbarth
\end{Author}
\begin{References}\relax
\url{http://tagcalling.mbgproject.org}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{sage.test}{sage.test}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
library(sagenhaft)
B6Hypo <- read.sage.library(system.file("data/B6HypothalHFI.sage",
                            package="sagenhaft")) 
E15post <- read.sage.library(system.file("data/E15postHFI.sage",
                             package="sagenhaft")) 
libcomp <- compare.lib.pair(B6Hypo, E15post)
plot(libcomp)
libcomp
\end{ExampleCode}
\end{Examples}

