\HeaderA{processCGH}{Process data in an MAList}{processCGH}
\keyword{file}{processCGH}
\begin{Description}\relax
This function takes object of class \code{MAList} and it re-orderes
and filters clones based on their mapping information and proportion missing. It also average duplicated clones and imputes missing values for clones
that are still NA after the filetering step.
\end{Description}
\begin{Usage}
\begin{verbatim}
processCGH(input, maxChromThreshold = 22, minChromThreshold
                 = 1, method.of.averaging = NULL, ID = "ID")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{input}] Object of class \code{\LinkA{MAList}{MAList}} or \code{\LinkA{RGList}{RGList}}
\item[\code{maxChromThreshold}] Chromosomes are ordered and numbered as
usual, except for X and Y chromosome, which in for Homo sapiens
genome have numbers 23 and 24 repsectivelly, in for Mus musculus 20
and 21, etc. Remove chromosomes from segmentation analysis which are
greater than this value.
\item[\code{minChromThreshold}] Chromosomes are ordered and numbered as
usual, except for X and Y chromosome, which in for Homo sapiens
genome have numbers 23 and 24 repsectivelly, in for Mus musculus 20
and 21, etc. Remove chromosomes from segmentation analysis which re
lower than this value.
\item[\code{method.of.averaging}] If left as the default no combining of replicate spots takes place.  Other wise this should specify a function which takes a vector of
duplicates and combines them into a single value.
\item[\code{ID}] Name of column in \code{RG\$genes} corresponding to the clone names. For most
data the default will work, however for affy data the
value for ID should be \code{"CloneName"}
\end{ldescription}
\end{Arguments}
\begin{Value}
Object of class \code{\LinkA{SegList}{SegList}}
\end{Value}
\begin{Author}\relax
Jane Fridlyand, Peter Dimitrov, John Marioni and Mike Smith
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{MAList}{MAList}}
\end{SeeAlso}

