\name{classifySVMsc}
\alias{classifySVMsc}

\title{
  Function to do discrimination analysis, by the search and choose method
}

\description{
  Function to search by groups of few genes, also called cliques, that
  can discriminate (or classify) between two distinct biological
  sample types using the Support Vector Machinnes method. This
  function uses the search and choose method.
}

\usage{
classifySVMsc(obj=NULL, sLabelID="Classification", func="wilcox.test",
              facToClass=NULL, gNameID="GeneName", geneGrp=1, path=NULL,
              nGenes=3, cliques=100)
}

\arguments{
  \item{obj}{object of class \code{\link{maiges}} to search the classifiers.}
  \item{sLabelID}{character string with the identification of the sample
    label to be used.}
  \item{func}{string specifying the function to be used to search by the
    initial one-dimensional classifiers, like 'wilcox.test' or 't.test'.}
  \item{facToClass}{named list with 2 character vectors specifying the
    samples to be compared. If NULL (default) the first 2 types of
    sLabelID are used.}
  \item{gNameID}{character string with the identification of gene label ID.}
  \item{geneGrp}{character or integer specifying the gene group to be
    tested (\code{colnames} of \code{GeneGrps} slot). If both \code{geneGrp} and
    \code{path} are NULL all genes are used. Defaults to 1 (first group).}
  \item{path}{character or integer specifying the gene network to be
    tested (\code{names} of \code{Paths} slot). If both \code{geneGrp}
    and \code{path} are NULL all genes are used. Defaults to NULL.}
  \item{nGenes}{integer specifying the number of genes in the clique, or
    classifier.}
  \item{cliques}{integer specifying the number of cliques or classifiers
    to be generated.}
}

\value{
  The result of this function is an object of class \code{\link{maigesClass}}.
}

\details{
  This function implements the method known as Search and choose
  proposed by Cristo (2003). If you want to use an exhaustive search use
  the function \code{\link{classifySVM}}.
  
  This method uses the function \code{\link[e1071]{svm}} from
  package \emph{e1071} to search classifiers by Support Vector
  Machines. It is possible to search by classifiers using Fisher's
  linear discriminant analysis and k nearest neighbours methods using
  the functions \code{\link{classifyLDAsc}} and
  \code{\link{classifyKNNsc}}, respectively.
}


\references{
  Cristo, E.B. Metodos Estatisticos na Analise de Experimentos de
  Microarray. Masther's thesis, Instituto de Matematica
  e Estatistica - Universidade de Sao Paulo, 2003 (in portuguese).
}

\seealso{
  \code{\link[e1071]{svm}}, \code{\link{classifySVM}},
  \code{\link{classifyLDAsc}} and \code{\link{classifyKNNsc}}.
}

\examples{
## Loading the dataset
data(gastro)

## Doing SVM classifier with 2 genes for the 6th gene group comparing
## the 2 categories from 'Type' sample label.
gastro.class = classifySVMsc(gastro.summ, sLabelID="Type",
  gNameID="GeneName", nGenes=2, geneGrp=1, cliques=10)
gastro.class

## To do classifier with 3 genes for the 6th gene group comparing
## normal vs adenocarcinomas from 'Tissue' sample label
gastro.class = classifySVMsc(gastro.summ, sLabelID="Tissue",
  gNameID="GeneName", nGenes=3, geneGrp=1, cliques=10,
  facToClass=list(Norm=c("Neso","Nest"), Ade=c("Aeso","Aest")))
}

\author{
  Elier B. Cristo, adapted by Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
}

\keyword{methods}