\HeaderA{plotSummaryProfile}{plotSummaryProfile}{plotSummaryProfile}
\keyword{hplot}{plotSummaryProfile}
\begin{Description}\relax
This function display the genomic events and tests for the differences
between groups if they are specified.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotSummaryProfile(aCGH.obj,
                   response = as.factor(rep("All", ncol(aCGH.obj))),
                   titles = unique(response[!is.na(response)]),
                   X = TRUE, Y = FALSE, maxChrom = 23,
                   chrominfo = human.chrom.info.Jul03,
                   num.plots.per.page = length(titles),
                   factor = 2.5, posThres=100, negThres=-0.75)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{aCGH.obj}] an object of aCGH class.
\item[\code{response}] phenotype to compare. defaults to all the samples being analyzed
together.

\item[\code{titles}] titles for the groups, defaults to the name of the \code{response}

\item[\code{X}] logical indicating whether X needs to be shown

\item[\code{Y}] logical indicating whether Y needs to be shown

\item[\code{maxChrom}] this parameter controls how many chromosomes will be
plotted, from 1 to maxChrom
\item[\code{chrominfo}] a chromosomal information associated with the mapping of the data

\item[\code{num.plots.per.page}] number of frequency plots per page. Default is the number of
groups

\item[\code{factor}] \code{factor} specifies the number by which experimental variability should be multiples. Used only when tumor specific variability in \code{aCGH.obj} is not NULL. Defaults to 2.5
\item[\code{posThres}] Threshold for gain. Set very high for homozygous deletion
\item[\code{negThres}] Threshold for homozygous deletion
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function utilizes output of the \code{\LinkA{find.genomic.events}{find.genomic.events}}
by plotting it and testing between groups. The test are performed
using kruskal-wallis rank test.
\end{Details}
\begin{SeeAlso}\relax
\code{\LinkA{aCGH}{aCGH}}
\code{\LinkA{find.genomic.events}{find.genomic.events}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(colorectal)

## Plotting summary of the sample profiles
plotSummaryProfile(colorectal)

\end{ExampleCode}
\end{Examples}

