\HeaderA{chromosome2integer}{Converts chromosome to integer or vice versa}{chromosome2integer}
\aliasA{integer2chromosome}{chromosome2integer}{integer2chromosome}
\keyword{manip}{chromosome2integer}
\begin{Description}\relax
Provides a standard way of converting chromosome annotation stored in
\code{SnpLevelSet} objects to the numeric class.
\end{Description}
\begin{Usage}
\begin{verbatim}
chromosome2integer(chrom)
integer2chromosome(chrom)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{chrom}] chromosome
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This is useful when sorting SNPs in an object by chromosome and
physical position -- ensures that the sorting is done in the same way
for different objects.

The function currently provides the following conversions:

"X" -\textgreater{} 23
"Y" -\textgreater{} 24
"XY" -\textgreater{} 25  
"M" -\textgreater{} 26
\end{Details}
\begin{Value}
\code{integer}
\code{character}
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}

