\HeaderA{runDNAcopy}{Results of segmenting an MAList data object using the DNAcopy library}{runDNAcopy}
\keyword{methods}{runDNAcopy}
\begin{Description}\relax
The results of segmenting data from copy number array experiments from
programs such as circular binary segmentation (CBS).  This function requires
the library \code{DNAcopy} to be loaded.
\end{Description}
\begin{Usage}
\begin{verbatim}
runDNAcopy(input, smooth.region=2, outlier.SD.scale = 4, smooth.SD.scale = 2, trim=0.025, alpha = 0.01, p.method = c("hybrid", 
    "perm"), kmax = 25, nmin = 200, window.size = NULL, overlap = 0.25, undo.splits = c("none", "prune", "sdundo"), 
    undo.prune = 0.05, undo.SD = 3)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{input}] An object of class \code{\LinkA{MAList}{MAList}} or \code{\LinkA{SegList}{SegList}}
\item[\code{smooth.region}] number of points to consider on the left and the
right of a point to detect it as an outlier.
\item[\code{outlier.SD.scale}] the number of SDs away from the nearest point
in the smoothing region to call a point an outlier.
\item[\code{smooth.SD.scale}] the number of SDs from the median in the
smoothing region where a smoothed point is positioned.
\item[\code{trim}] proportion of data to be trimmed for variance calculation
for smoothing outliers and undoing splits based on SD.
\item[\code{alpha}] significance levels for the test to accept change-points.
\item[\code{p.method}] method used for p-value computation.  For the "perm"
method the p-value is based on full permutation.  For the "hybrid"
method the maximum over the entire region is split into maximum of
max over small segments and max over the rest.  Approximation is
used for the larger segment max. Default is hybrid.
\item[\code{kmax}] the maximum width of smaller segment for permutation
in the hybrid method.
\item[\code{nmin}] the minimum length of data for which the approximation of
maximum statistic is used under the hybrid method.
\item[\code{window.size}] size of window used to speed up computations when
segment size is too large.  Default is NULL (whole segment used).
If p.method is hybrid then this is set to NULL.
\item[\code{overlap}] proportion of data that overlap for adjacent windows.
\item[\code{undo.splits}] A character string specifying how change-points are
to be undone, if at all.  Default is "none".  Other choices are
"prune", which uses a sum of squares criterion, and "sdundo", which 
undoes splits that are not at least this many SDs apart.
\item[\code{undo.prune}] the proportional increase in sum of squares allowed
when eliminating splits if undo.splits="prune".
\item[\code{undo.SD}] the number of SDs between means to keep a split if
undo.splits="sdundo".
\end{ldescription}
\end{Arguments}
\begin{Value}
The function returns an object of class \code{\LinkA{SegList}{SegList}}
\end{Value}
\begin{Author}\relax
Mike Smith, based upon DNAcopy help files written by E. S. Venkatraman and Adam Olshen
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{segment}{segment}}
\code{\LinkA{MAList}{MAList}}
\code{\LinkA{runHomHMM}{runHomHMM}}
\code{\LinkA{runGLAD}{runGLAD}}
\code{\LinkA{SegList}{SegList}}
\end{SeeAlso}

