\HeaderA{maigesActMod-class}{maigesActMod class, store results of functional classification of gene
groups}{maigesActMod.Rdash.class}
\aliasA{maigesActMod}{maigesActMod-class}{maigesActMod}
\keyword{classes}{maigesActMod-class}
\begin{Description}\relax
This class defines a structure to store the results of functional
classification of gene groups (or modules) that was proposed by Segal
et al. (2004), see the reference below. Objects of this type are
generated by calling the function \code{\LinkA{activeMod}{activeMod}}.
\end{Description}
\begin{Details}\relax
Objects of this class are produced by calling the function
\code{\LinkA{activeMod}{activeMod}} over an object of class \code{\LinkA{maiges}{maiges}}
to search for gene groups that present numbers of genes induced or
repressed greater than the expected by chance in biological sample
types of interest. This is done according to the model proposed by
Segal et al. (2004), described below.
\end{Details}
\begin{Section}{Slots}
\describe{
\item[\code{modBySamp}:] numerical matrix containing the fraction of
genes activated (or negative fraction of genes repressed) for all
chips. The rows and columns of the matrix represents the chips and
the gene groups used, respectively.
\item[\code{modByCond}:] numerical matrix storing the fraction (or
negative fraction) of different sample types that presents
alteration in the gene groups tested. The rows and columns
represents the sample types and gene groups, respectively.
\item[\code{globalScore}:] list with the same length as the number
of gene groups containing matrices with the genes as rows and 2
columns. The first column gives a global score that measure the
consistency of the classification of the gene and the group, the
second column gives the p-value for this score, as described in
Segal et al. (2004).
\item[\code{tissueScore}:] a list similar to the previous one, but
having arrays of 3 dimensions that gives scores similar to that
one described above, but relating only to each specific sample
type. Note that this new score was implemented in this package and
not in the original Segal's work.
\item[\code{Date}:] character string giving the date and time that
the object was generated.
\item[\code{V.info}:] list containg three characters. The first one is
a string containing the R version used when the object was
created. The second is a char vector with base packages and the
last one is another char vector with additional packages and
version numbers.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[image] \code{signature(x = 'maigesActMod')}: image method for
\code{\LinkA{maigesActMod}{maigesActMod}} class. Display colour representation of
the fractions of gene groups induced and repressed.
\item[plot] \code{signature(x = 'maigesActMod')}: plot method for
\code{\LinkA{maigesActMod}{maigesActMod}} class. Do the same as image.
\item[print] \code{signature(x = 'maigesActMod')}: print method for
\code{\LinkA{maigesActMod}{maigesActMod}} class.
\item[show] \code{signature(x = 'maigesActMod')}: show method for
\code{\LinkA{maigesActMod}{maigesActMod}} class.
\item[summary] \code{signature(x = 'maigesActMod')}: summary method for
\code{\LinkA{maigesActMod}{maigesActMod}} class.
}
\end{Section}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{References}\relax
Segal, E.; Friedman, N.; Koller, D. and Regev, A. A module map showing
conditional activity of expression modules in cancer. \bold{Nature
Genetics}, 36, 1090-1098, 2004. (\url{http://www.nature.com/ng/journal/v36/n10/abs/ng1434.html})
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{activeMod}{activeMod}}.
\end{SeeAlso}

