\HeaderA{stat.gnames}{Sort Genes According to the Value of a Statistic}{stat.gnames}
\keyword{misc}{stat.gnames}
\begin{Description}\relax
Lists genes and corresponding statistics in decreasing order of the
statistics. This function applies to any type of statistic, including
log ratios, one and two-sample t-statistics, and F-statistics. Missing
values are ignored, as in \code{\LinkA{sort}{sort}(..., na.last=NA)}.
\end{Description}
\begin{Usage}
\begin{verbatim}
stat.gnames(x, gnames, crit=0.05)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a numeric vector containing the statistics for each
gene. Missing values (NAs) are allowed. 
\item[\code{gnames}] a character vector containing the gene names.
\item[\code{crit}] specifies the number of genes to be returned. If crit <
1, the crit*100\% genes with the largest x values are listed. If crit
>= 1, the crit genes with the largest x values are listed. 
\end{ldescription}
\end{Arguments}
\begin{Value}
List containing the following components 
\begin{ldescription}
\item[\code{gnames}] gene names sorted in decreasing order of the
statistics in x.
\item[\code{t}] statistics sorted in decreasing order.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Yee Hwa Yang, \email{yeehwa@stat.berkeley.edu} \\
Sandrine Dudoit, \email{sandrine@stat.berkeley.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{stat.t2}{stat.t2}}, \code{\LinkA{order}{order}}, \code{\LinkA{sort}{sort}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Calculating log ratio and performing a t test.
data(MouseArray)
## mouse.setup <- init.grid()
## mouse.data <- init.data() ## see \emph{init.data}
mouse.lratio <- stat.ma(mouse.data, mouse.setup)
cl <- c(rep(1,3), rep(2,3))
mouse.t2 <- stat.t2(mouse.lratio, cl)

## Looking at gene names
## Finding the top 10 t-statistics
stat.gnames(abs(mouse.t2$t), mouse.gnames, crit=10)

## Finding the top 1
stat.gnames(abs(mouse.t2$t), mouse.gnames, crit=0.01)

## Finding the 10 extreme M values in the first slide
stat.gnames(abs(mouse.lratio$M[, 1]), mouse.gnames, crit=10)
\end{ExampleCode}
\end{Examples}

