\HeaderA{calculateCnSE}{Calculates copy number standard errors}{calculateCnSE}
\keyword{manip}{calculateCnSE}
\begin{Description}\relax
Calculates SNP-specific standard errors for copy number using a reference set.
\end{Description}
\begin{Usage}
\begin{verbatim}
calculateCnSE(object, referenceSet, epsilon = 0.1)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] An object of class \code{SnpCopyNumberSet} or
\code{oligoSnpSet}.  
\item[\code{referenceSet}] An object of class \code{SnpCopyNumberSet} or
\code{oligoSnpSet}. If missing, this function uses the samples in
the \code{object} to estimate across sample standard deviations 
\item[\code{epsilon}] minimum standard error
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Calculates SNP-specific standard errors from a reference distribution
as the product of the within copy number standard deviation of the
sample (test set) and the across samples standard deviation from a
reference set.  The across samples standard deviation is scaled by the
median (e.g., across sample sd = across sample sd/ median(across
sample sd)).
\end{Details}
\begin{Value}
A matrix of standard errors
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}

