\HeaderA{make.chromOrd}{Make a chromOrd object}{make.chromOrd}
\keyword{utilities}{make.chromOrd}
\begin{Description}\relax
This function makes a chromOrd object.
\end{Description}
\begin{Usage}
\begin{verbatim}
make.chromOrd(genome, gnames)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{genome}] A character string. 
\item[\code{gnames}] A character vector of the genes to be selected. 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function reads in a lot of annotation data and creates a list
with one element for each chromosome. The elements of this list are
indices indicating the order of the genes that are on that chromosome
(and in the annotation data set being used).
\end{Details}
\begin{Value}
A list of chromOrd type. One element for each chromosome. Suitable for
reordering other values according to the chromosomal location.
\end{Value}
\begin{Author}\relax
Robert Gentleman
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{amplicon.plot}{amplicon.plot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  data(sample.ExpressionSet)
  make.chromOrd("hgu95A", featureNames(sample.ExpressionSet))
\end{ExampleCode}
\end{Examples}

