\HeaderA{aCGH.process}{Process data in aCGH object}{aCGH.process}
\keyword{file}{aCGH.process}
\begin{Description}\relax
This function takes object of class \code{aCGH}, and filters clones based on their mapping information and proportion missing. It also average duplicated clones and reports quality statistic.
\end{Description}
\begin{Usage}
\begin{verbatim}
aCGH.process(aCGH.obj, chrom.remove.threshold = 24,
                 prop.missing = 0.25, sample.quality.threshold = 0.4,
                 unmapScreen=TRUE, dupRemove = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{aCGH.obj}] Object of class aCGH
\item[\code{chrom.remove.threshold}] 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.
\item[\code{prop.missing}] Clones are screened out and if the proportion
missing in the samples is \code{prop.missing} they are removed.
\item[\code{sample.quality.threshold}] Mark those samples that have their
proportion of missing values \code{sample.quality.threshold}.
\item[\code{unmapScreen}] Indicator for whether clones with incomplete mapping information should be removed from the dataset. Note that leaving them in may cause plotting routines fail. Defaults to TRUE
\item[\code{dupRemove}] Indicator for whether clones with duplicate names should be averaged and removed from the dataset leaving only one occurence of each duplicated set.Defaults to TRUE
\end{ldescription}
\end{Arguments}
\begin{Value}
Object of class \code{aCGH}.
\end{Value}
\begin{Author}\relax
Jane Fridlyand, Peter Dimitrov
\end{Author}
\begin{SeeAlso}\relax
\code{aCGH}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

datadir <- system.file(package = "aCGH")
datadir <- paste(datadir, "/examples", sep="")

clones.info <-
      read.table(file = file.path(datadir, "clones.info.ex.txt"),
                 header = TRUE, sep = "\t", quote="", comment.char="")
log2.ratios <-
      read.table(file = file.path(datadir, "log2.ratios.ex.txt"),
                 header = TRUE, sep = "\t", quote="", comment.char="")
pheno.type <- read.table(file = file.path(datadir, "pheno.type.ex.txt"),header = TRUE, sep = "\t", quote="", comment.char="")
ex.acgh <- create.aCGH(log2.ratios, clones.info, pheno.type)
ex.acgh <-
    aCGH.process(ex.acgh, chrom.remove.threshold = 23, prop.missing = .25, 
sample.quality.threshold = .4, unmapScreen=TRUE, dupRemove = FALSE)
ex.acgh

\end{ExampleCode}
\end{Examples}

