\HeaderA{maigesRelNetB-class}{maigesRelNetB class, store results of relevance network analysis (Butte's method)}{maigesRelNetB.Rdash.class}
\aliasA{maigesRelNetB}{maigesRelNetB-class}{maigesRelNetB}
\keyword{classes}{maigesRelNetB-class}
\begin{Description}\relax
This class defines a structure to store the results of relevance network analysis,
using a method that was proposed by Butte et al. (2000), see the
reference below. Objects of this type are generated calling
the function \code{\LinkA{relNetworkB}{relNetworkB}}.
\end{Description}
\begin{Details}\relax
Objects of this class are produced by calling the function
\code{\LinkA{relNetworkB}{relNetworkB}} over an object of class \code{\LinkA{maiges}{maiges}}
to search for pairs of genes with significant correlation values in a
specific sample type, according to the method proposed by Butte et
al. (2000).
\end{Details}
\begin{Section}{Slots}
\describe{
\item[\code{W}:] numeric matrix giving the W values of the genes
tested. This information is useful for doing plots representing the
correlation coefficient values.
\item[\code{Corr}:] numerical square matrix that store the
correlation coefficient values between all pair of genes tested.
\item[\code{Pval}:] numerical square matrix that store the p-value
for each correlation value between the pairs of genes.
\item[\code{maxB}:] numerical square matrix that store the maximum
(in absolute value) of the correlation values calculated by
permutation values, as described by Butte et al. (2000).
\item[\code{types}:] character vector giving the name of sample
type tested.
\item[\code{Slabel}:] string with the sample label used to define
the sample types tested.
\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 = 'maigesRelNetB')}: image method for
\code{\LinkA{maigesRelNetB}{maigesRelNetB}} class. Display colour representation of
the correlation matrix.
\item[plot] \code{signature(x = 'maigesRelNetB')}: plot method for
\code{\LinkA{maigesRelNetB}{maigesRelNetB}} class. Display a circular graph
representing the relevance network.
\item[print] \code{signature(x = 'maigesRelNetB')}: print method for
\code{\LinkA{maigesRelNetB}{maigesRelNetB}} class.
\item[show] \code{signature(x = 'maigesRelNetB')}: show method for
\code{\LinkA{maigesRelNetB}{maigesRelNetB}} class.
\item[summary] \code{signature(x = 'maigesRelNetB')}: summary method for
\code{\LinkA{maigesRelNetB}{maigesRelNetB}} class.
}
\end{Section}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{References}\relax
Butte, A.J.; Tamayo, P.; Slonim, D.; Golub, T.R. and Kohane,
I.S. Discovering functional relationships between RNA expression and
chemotherapeutic susceptibility using relevance networks. \bold{PNAS}, 97,
12182-12186, 2000. (\url{http://www.pnas.org/cgi/content/full/97/22/12182})
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{relNetworkB}{relNetworkB}}.
\end{SeeAlso}

