\HeaderA{getImat}{Generate an indicator matrix}{getImat}
\keyword{htest}{getImat}
\begin{Description}\relax
This function is used to generate an indicator matrix as an input to
the pcot2 function. The gene category indicator matrix indicates
presence or absence of genes in pre-defined gene sets
(e.g., gene pathways). The indicator matrix contains rows representing
gene identifiers of genes present in the expression data and columns
representing pre-defined group names. A value of 1 indicates the
presence of a gene and 0 indicates the absence for the gene in a
particular group.
\end{Description}
\begin{Usage}
\begin{verbatim}
getImat(x, pathlist, ms = 10)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] A matrix with no missing values; Each row represents a gene
and each column represents a sample.
\item[\code{pathlist}] A list of gene sets. 
\item[\code{ms}] The minimum gene set size. Gene sets containing less
than this number of genes will be excluded from the analysis.
\end{ldescription}
\end{Arguments}
\begin{Value}
An indicator matrix is returned. The matrix value is 1 (gene in) or 0 (gene out)
\end{Value}
\begin{Author}\relax
Sarah Song and Mik Black
\end{Author}
\begin{References}\relax
S.Song and M.Black (2006) PCOT2: an R package for assessing
expression changes in groups of related genes. Submitted to Bioinformatics.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{pcot2}{pcot2}},\code{\LinkA{corplot}{corplot}},\code{\LinkA{corplot2}{corplot2}},\code{\LinkA{aveProbe}{aveProbe}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
library(multtest)
library(hu6800)  
data(golub)
rownames(golub) <- golub.gnames[,3]
colnames(golub) <- golub.cl
KEGG.list <- as.list(hu6800PATH)
imat <- getImat(golub, KEGG.list, ms=10) 
\end{ExampleCode}
\end{Examples}

