\Header{pamr.listgenes}{A function to list the genes that survive the thresholding,
from the nearest shrunken centroid classifier}
\begin{Description}\relax
A function to list the genes that survive the thresholding,
from the nearest shrunken centroid classifier produced by pamr.train
\end{Description}
\begin{Usage}
\begin{verbatim}
pamr.listgenes(fit, data, threshold, genenames=FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fit}] The result of a call to pamr.train
\item[\code{data}] The input data.  In the same format as the input data for
pamr.train
\item[\code{threshold}] The desired threshold value
\item[\code{genenames}] Include genenames in the list? If yes, they
are taken from "data". Default is false (geneid is always included
in the list).
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{pamr.listgenes} List the geneids, and standardized centroids for
each class, for genes surviving at the given threshold.
\end{Details}
\begin{Author}\relax
Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu
\end{Author}
\begin{References}\relax
\end{References}
\begin{Examples}
\begin{ExampleCode}
set.seed(120)
x <- matrix(rnorm(1000*20),ncol=20)
y <- sample(c(1:4),size=20,replace=TRUE)
mydata <- list(x=x,y=y,geneid=as.character(1:1000))
mytrain <-   pamr.train(mydata)
mycv <- pamr.cv(mytrain,mydata)
pamr.listgenes(mytrain, mydata, threshold=1.6)
 
\end{ExampleCode}
\end{Examples}

